Next Issue
Previous Issue

E-Mail Alert

Add your e-mail address to receive forthcoming issues of this journal:

Journal Browser

Journal Browser

Table of Contents

Int. J. Mol. Sci., Volume 15, Issue 1 (January 2014), Pages 1-1685

  • Issues are regarded as officially published after their release is announced to the table of contents alert mailing list.
  • You may sign up for e-mail alerts to receive table of contents of newly released issues.
  • PDF is the official format for papers published in both, html and pdf forms. To view the papers in pdf format, click on the "PDF Full-text" link, and use the free Adobe Readerexternal link to open them.
View options order results:
result details:
Displaying articles 1-100
Export citation of selected articles as:

Editorial

Jump to: Research, Review, Other

Open AccessEditorial International Journal of Molecular Science Best Paper Award 2014
Int. J. Mol. Sci. 2014, 15(1), 1683-1685; doi:10.3390/ijms15011683
Received: 20 January 2014 / Revised: 20 January 2014 / Accepted: 21 January 2014 / Published: 22 January 2014
Cited by 2 | PDF Full-text (145 KB) | HTML Full-text | XML Full-text
Abstract
International Journal of Molecular Science is instituting an annual award to recognize outstanding papers in the area of chemistry, molecular physics and molecular biology published in International Journal of Molecular Science. We are pleased to announce the third “International Journal [...] Read more.
International Journal of Molecular Science is instituting an annual award to recognize outstanding papers in the area of chemistry, molecular physics and molecular biology published in International Journal of Molecular Science. We are pleased to announce the third “International Journal of Molecular Science Best Paper Award” for 2014 [1,2]. Nominations were made by the Section Editors-in-Chief of International Journal of Molecular Science from all papers published in 2010. [...] Full article
Figures

Research

Jump to: Editorial, Review, Other

Open AccessArticle Effect and Mechanism of Mitomycin C Combined with Recombinant Adeno-Associated Virus Type II against Glioma
Int. J. Mol. Sci. 2014, 15(1), 1-14; doi:10.3390/ijms15010001
Received: 29 July 2013 / Revised: 9 December 2013 / Accepted: 9 December 2013 / Published: 19 December 2013
Cited by 2 | PDF Full-text (1617 KB) | HTML Full-text | XML Full-text
Abstract
The effect of chemotherapy drug Mitomycin C (MMC) in combination with recombinant adeno-associated virus II (rAAV2) in cancer therapy was investigated, and the mechanism of MMC affecting rAAV2’s bioactivity was also studied. The combination effect was evaluated by the level of GFP [...] Read more.
The effect of chemotherapy drug Mitomycin C (MMC) in combination with recombinant adeno-associated virus II (rAAV2) in cancer therapy was investigated, and the mechanism of MMC affecting rAAV2’s bioactivity was also studied. The combination effect was evaluated by the level of GFP and TNF expression in a human glioma cell line, and the mechanism of MMC effects on rAAV mediated gene expression was investigated by AAV transduction related signal molecules. C57 and BALB/c nude mice were injected with rAAV-EGFP or rAAV-TNF alone, or mixed with MMC, to evaluate the effect of MMC on AAV-mediated gene expression and tumor suppression. MMC was shown to improve the infection activity of rAAV2 both in vitro and in vivo. Enhancement was found to be independent of initial rAAV2 receptor binding stage or subsequent second-strand synthesis of target DNA, but was related to cell cycle retardation followed by blocked genome degradation. In vivo injection of MMC combined with rAAV2 into the tumors of the animals resulted in significant suppression of tumor growth. It was thus demonstrated for the first time that MMC could enhance the expression level of the target gene mediated by rAAV2. The combination of rAAV2 and MMC may be a promising strategy in cancer therapy. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Heat-killed VSL#3 Ameliorates Dextran Sulfate Sodium (DSS)-Induced Acute Experimental Colitis in Rats
Int. J. Mol. Sci. 2014, 15(1), 15-28; doi:10.3390/ijms15010015
Received: 10 October 2013 / Revised: 9 December 2013 / Accepted: 10 December 2013 / Published: 19 December 2013
Cited by 3 | PDF Full-text (1181 KB) | HTML Full-text | XML Full-text
Abstract
To determine the effects of heat-killed VSL#3 (B. breve, B. longum and B. infantis; L. plantarum, L. bulgaricus, L. casei and L. acidophilus; S. salivarius subsp. thermophilus) therapy in the dextran sulfate sodium (DSS)-induced acute [...] Read more.
To determine the effects of heat-killed VSL#3 (B. breve, B. longum and B. infantis; L. plantarum, L. bulgaricus, L. casei and L. acidophilus; S. salivarius subsp. thermophilus) therapy in the dextran sulfate sodium (DSS)-induced acute experimental colitis in rats. Acute experimental colitis was induced in rats by 5% DSS and freely drink for seven days. Beginning on Day 8, rats underwent gavage once daily for seven days with heat-killed probiotic VSL#3 (0.6 g/kg/day), colonic damage was evaluated histologically and biochemically seven days after gavage. Expression of inflammatory related mediators (STAT3, P-STAT3) and cytokines (IL-6, IL-23, TGFβ) in colonic tissue were detected. The results revealed that heat-killed and live VSL#3 have identical anti-inflammatory properties by the assessed DAI (disease activity index), colon length, histological tissue and MPO activity. Heat-killed and live VSL#3 results in reduced IL-6, IL-23, TGFβ, STAT3 and P-STAT3 expression in colonic tissue. Heat-killed and live VSL#3 have showed the similar anti-inflammatory activity by inhibiting IL-6/STAT3 pathway in the DSS-induced acute experimental colitis in rats. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle The C-Terminal Region of G72 Increases D-Amino Acid Oxidase Activity
Int. J. Mol. Sci. 2014, 15(1), 29-43; doi:10.3390/ijms15010029
Received: 28 October 2013 / Revised: 28 November 2013 / Accepted: 6 December 2013 / Published: 20 December 2013
Cited by 5 | PDF Full-text (1078 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The schizophrenia-related protein G72 plays a unique role in the regulation of D-amino acid oxidase (DAO) in great apes. Several psychiatric diseases, including schizophrenia and bipolar disorder, are linked to overexpression of DAO and G72. Whether G72 plays a positive or negative [...] Read more.
The schizophrenia-related protein G72 plays a unique role in the regulation of D-amino acid oxidase (DAO) in great apes. Several psychiatric diseases, including schizophrenia and bipolar disorder, are linked to overexpression of DAO and G72. Whether G72 plays a positive or negative regulatory role in DAO activity, however, has been controversial. Exploring the molecular basis of the relationship between G72 and DAO is thus important to understand how G72 regulates DAO activity. We performed yeast two-hybrid experiments and determined enzymatic activity to identify potential sites in G72 involved in binding DAO. Our results demonstrate that residues 123–153 and 138–153 in the long isoform of G72 bind to DAO and enhance its activity by 22% and 32%, respectively. A docking exercise indicated that these G72 peptides can interact with loops in DAO that abut the entrance of the tunnel that substrate and cofactor must traverse to reach the active site. We propose that a unique gating mechanism underlies the ability of G72 to increase the activity of DAO. Because upregulation of DAO activity decreases d-serine levels, which may lead to psychiatric abnormalities, our results suggest a molecular mechanism involving interaction between DAO and the C-terminal region of G72 that can regulate N-methyl-d-aspartate receptor-mediated neurotransmission. Full article
(This article belongs to the collection Proteins and Protein-Ligand Interactions)
Open AccessArticle Efficacy and Feasibility of the Epithelial Cell Adhesion Molecule (EpCAM) Immunomagnetic Cell Sorter for Studies of DNA Methylation in Colorectal Cancer
Int. J. Mol. Sci. 2014, 15(1), 44-57; doi:10.3390/ijms15010044
Received: 7 November 2013 / Revised: 10 December 2013 / Accepted: 13 December 2013 / Published: 20 December 2013
Cited by 3 | PDF Full-text (505 KB) | HTML Full-text | XML Full-text
Abstract
The aim of this work was to assess the impact on measurements of methylation of a panel of four cancer gene promoters of purifying tumor cells from colorectal tissue samples using the epithelial cell adhesion molecule (EpCAM)-immunomagnetic cell enrichment approach. We observed [...] Read more.
The aim of this work was to assess the impact on measurements of methylation of a panel of four cancer gene promoters of purifying tumor cells from colorectal tissue samples using the epithelial cell adhesion molecule (EpCAM)-immunomagnetic cell enrichment approach. We observed that, on average, methylation levels were higher in enriched cell fractions than in the whole tissue, but the difference was significant only for one out of four studied genes. In addition, there were strong correlations between methylation values for individual samples of whole tissue and the corresponding enriched cell fractions. Therefore, assays on whole tissue are likely to provide reliable estimates of tumor-specific methylation of cancer genes. However, tumor cell tissue separation using immunomagnetic beads could, in some cases, give a more accurate value of gene promoter methylation than the analysis of the whole cancer tissue, although relatively expensive and time-consuming. The efficacy and feasibility of the immunomagnetic cell sorting for methylation studies are discussed. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Chimeric Mice with Humanized Livers: A Unique Tool for in Vivo and in Vitro Enzyme Induction Studies
Int. J. Mol. Sci. 2014, 15(1), 58-74; doi:10.3390/ijms15010058
Received: 1 November 2013 / Revised: 5 December 2013 / Accepted: 6 December 2013 / Published: 20 December 2013
Cited by 8 | PDF Full-text (606 KB) | HTML Full-text | XML Full-text
Abstract
We performed in vivo and in vitro studies to determine the induction of human cytochrome P450 (CYP) using chimeric mice with humanized liver (PXB-mice®) and human hepatocytes isolated from the PXB-mice (PXB-cells), which were derived from the same donor. For [...] Read more.
We performed in vivo and in vitro studies to determine the induction of human cytochrome P450 (CYP) using chimeric mice with humanized liver (PXB-mice®) and human hepatocytes isolated from the PXB-mice (PXB-cells), which were derived from the same donor. For the in vivo study, PXB-mice were injected with 3-methylcholanthrene (3-MC, 2 or 20 mg/kg) or rifampicin (0.1 or 10 mg/kg) for four days. For the in vitro study, PXB-cells were incubated with 3-MC (10, 50, or 250 ng/mL) or with rifampicin (5 or 25 μg/mL). The CYP1A1 and 1A2, and CYP3A4 mRNA expression levels increased significantly in the PXB-mouse livers with 20 mg/kg of 3-MC (Cmax, 12.2 ng/mL), and 10 mg/kg rifampicin (Cmax, 6.9 µg/mL), respectively. The CYP1A1 mRNA expression level increased significantly in PXB-cells with 250 ng/mL of 3-MC, indicating lower sensitivity than in vivo. The CYP1A2 and CYP3A4 mRNA expression levels increased significantly with 50 ng/mL of 3-MC, and 5 μg/mL of rifampicin, respectively, which indicated that the sensitivities were similar between in vivo and in vitro studies. In conclusion, PXB-mice and PXB-cells provide a robust model as an intermediate between in vivo and in vitro human metabolic enzyme induction studies. Full article
(This article belongs to the Special Issue Xenobiotic Metabolism)
Open AccessArticle Interaction of Classical Platinum Agents with the Monomeric and Dimeric Atox1 Proteins: A Molecular Dynamics Simulation Study
Int. J. Mol. Sci. 2014, 15(1), 75-99; doi:10.3390/ijms15010075
Received: 1 November 2013 / Revised: 5 December 2013 / Accepted: 12 December 2013 / Published: 20 December 2013
Cited by 2 | PDF Full-text (2474 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
We carried out molecular dynamics simulations and free energy calculations for a series of binary and ternary models of the cisplatin, transplatin and oxaliplatin agents binding to a monomeric Atox1 protein and a dimeric Atox1 protein to investigate their interaction mechanisms. All [...] Read more.
We carried out molecular dynamics simulations and free energy calculations for a series of binary and ternary models of the cisplatin, transplatin and oxaliplatin agents binding to a monomeric Atox1 protein and a dimeric Atox1 protein to investigate their interaction mechanisms. All three platinum agents could respectively combine with the monomeric Atox1 protein and the dimeric Atox1 protein to form a stable binary and ternary complex due to the covalent interaction of the platinum center with the Atox1 protein. The results suggested that the extra interaction from the oxaliplatin ligand–Atox1 protein interface increases its affinity only for the OxaliPt + Atox1 model. The binding of the oxaliplatin agent to the Atox1 protein might cause larger deformation of the protein than those of the cisplatin and transplatin agents due to the larger size of the oxaliplatin ligand. However, the extra interactions to facilitate the stabilities of the ternary CisPt + 2Atox1 and OxaliPt + 2Atox1 models come from the α1 helices and α2-β4 loops of the Atox1 protein–Atox1 protein interface due to the cis conformation of the platinum agents. The combinations of two Atox1 proteins in an asymmetric way in the three ternary models were analyzed. These investigations might provide detailed information for understanding the interaction mechanism of the platinum agents binding to the Atox1 protein in the cytoplasm. Full article
(This article belongs to the collection Proteins and Protein-Ligand Interactions)
Figures

Open AccessArticle Synthesis and Characterization of β-Cyclodextrin Functionalized Ionic Liquid Polymer as a Macroporous Material for the Removal of Phenols and As(V)
Int. J. Mol. Sci. 2014, 15(1), 100-119; doi:10.3390/ijms15010100
Received: 22 August 2013 / Revised: 14 October 2013 / Accepted: 31 October 2013 / Published: 23 December 2013
Cited by 5 | PDF Full-text (1558 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
β-Cyclodextrin-ionic liquid polymer (CD-ILP) was first synthesized by functionalized β-cyclodextrin (CD) with 1-benzylimidazole (BIM) to form monofunctionalized CD (βCD-BIMOTs) and was further polymerized using a toluene diisocyanate (TDI) linker to form insoluble CD-ILP (βCD-BIMOTs-TDI). The βCD-BIMOTs-TDI polymer was characterized using various tools [...] Read more.
β-Cyclodextrin-ionic liquid polymer (CD-ILP) was first synthesized by functionalized β-cyclodextrin (CD) with 1-benzylimidazole (BIM) to form monofunctionalized CD (βCD-BIMOTs) and was further polymerized using a toluene diisocyanate (TDI) linker to form insoluble CD-ILP (βCD-BIMOTs-TDI). The βCD-BIMOTs-TDI polymer was characterized using various tools and the results obtained were compared with those derived from the native β-cyclodextrin polymer (βCD-TDI). The SEM result shows that the presence of ionic liquid (IL) increases the pore size, while the thermo gravimetric analysis (TGA) result shows that the presence of IL increases the stability of the polymer. Meanwhile, Brunauer-Emmett-Teller (BET) results show that βCD-BIMOTs-TDI polymer has 1.254 m2/g surface areas and the Barret-Joyner-Halenda (BJH) pore size distribution result reveals that the polymer exhibits macropores with a pore size of 77.66 nm. Preliminary sorption experiments were carried out and the βCD-BIMOTs-TDI polymer shows enhanced sorption capacity and high removal towards phenols and As(V). Full article
(This article belongs to the Special Issue Synthesis, Characterization and Application of Supramolecular Systems)
Figures

Open AccessArticle Genome-Wide Analysis of the Cyclin Gene Family in Tomato
Int. J. Mol. Sci. 2014, 15(1), 120-140; doi:10.3390/ijms15010120
Received: 31 October 2013 / Revised: 16 December 2013 / Accepted: 16 December 2013 / Published: 23 December 2013
Cited by 5 | PDF Full-text (1729 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Cyclins play important roles in cell division and cell expansion. They also interact with cyclin-dependent kinases to control cell cycle progression in plants. Our genome-wide analysis identified 52 expressed cyclin genes in tomato. Phylogenetic analysis of the deduced amino sequences of tomato [...] Read more.
Cyclins play important roles in cell division and cell expansion. They also interact with cyclin-dependent kinases to control cell cycle progression in plants. Our genome-wide analysis identified 52 expressed cyclin genes in tomato. Phylogenetic analysis of the deduced amino sequences of tomato and Arabidopsis cyclin genes divided them into 10 types, A-, B-, C-, D-, H-, L-, T-, U-, SDS- and J18. Pfam analysis indicated that most tomato cyclins contain a cyclin-N domain. C-, H- and J18 types only contain a cyclin-C domain, and U-type cyclins contain another potential cyclin domain. All of the cyclin genes are distributed throughout the tomato genome except for chromosome 8, and 30 of them were found to be segmentally duplicated; they are found on the duplicate segments of chromosome 1, 2, 3, 4, 5, 6, 10, 11 and 12, suggesting that tomato cyclin genes experienced a mass of segmental duplication. Quantitative real-time polymerase chain reaction analysis indicates that the expression patterns of tomato cyclin genes were significantly different in vegetative and reproductive stages. Transcription of most cyclin genes can be enhanced or repressed by exogenous application of gibberellin, which implies that gibberellin maybe a direct regulator of cyclin genes. The study presented here may be useful as a guide for further functional research on tomato cyclins. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Figures

Open AccessArticle A Human XPC Protein Interactome—A Resource
Int. J. Mol. Sci. 2014, 15(1), 141-158; doi:10.3390/ijms15010141
Received: 6 November 2013 / Revised: 12 December 2013 / Accepted: 17 December 2013 / Published: 23 December 2013
Cited by 11 | PDF Full-text (382 KB) | HTML Full-text | XML Full-text
Abstract
Global genome nucleotide excision repair (GG-NER) is responsible for identifying and removing bulky adducts from non-transcribed DNA that result from damaging agents such as UV radiation and cisplatin. Xeroderma pigmentosum complementation group C (XPC) is one of the essential damage recognition proteins [...] Read more.
Global genome nucleotide excision repair (GG-NER) is responsible for identifying and removing bulky adducts from non-transcribed DNA that result from damaging agents such as UV radiation and cisplatin. Xeroderma pigmentosum complementation group C (XPC) is one of the essential damage recognition proteins of the GG-NER pathway and its dysfunction results in xeroderma pigmentosum (XP), a disorder involving photosensitivity and a predisposition to cancer. To better understand the identification of DNA damage by XPC in the context of chromatin and the role of XPC in the pathogenesis of XP, we characterized the interactome of XPC using a high throughput yeast two-hybrid screening. Our screening showed 49 novel interactors of XPC involved in DNA repair and replication, proteolysis and post-translational modifications, transcription regulation, signal transduction, and metabolism. Importantly, we validated the XPC-OTUD4 interaction by co-IP and provided evidence that OTUD4 knockdown in human cells indeed affects the levels of ubiquitinated XPC, supporting a hypothesis that the OTUD4 deubiquitinase is involved in XPC recycling by cleaving the ubiquitin moiety. This high-throughput characterization of the XPC interactome provides a resource for future exploration and suggests that XPC may have many uncharacterized cellular functions. Full article
(This article belongs to the collection Proteins and Protein-Ligand Interactions)
Open AccessArticle Advanced Glycation End Product-Induced Astrocytic Differentiation of Cultured Neurospheres through Inhibition of Notch-Hes1 Pathway-Mediated Neurogenesis
Int. J. Mol. Sci. 2014, 15(1), 159-170; doi:10.3390/ijms15010159
Received: 23 November 2013 / Revised: 3 December 2013 / Accepted: 13 December 2013 / Published: 23 December 2013
Cited by 5 | PDF Full-text (1241 KB) | HTML Full-text | XML Full-text
Abstract
This study aims to investigate the roles of the Notch-Hes1 pathway in the advanced glycation end product (AGE)-mediated differentiation of neural stem cells (NSCs). We prepared pLentiLox3.7 lentiviral vectors that express short hairpin RNA (shRNA) against Notch1 and transfected it into NSCs. [...] Read more.
This study aims to investigate the roles of the Notch-Hes1 pathway in the advanced glycation end product (AGE)-mediated differentiation of neural stem cells (NSCs). We prepared pLentiLox3.7 lentiviral vectors that express short hairpin RNA (shRNA) against Notch1 and transfected it into NSCs. Cell differentiation was analyzed under confocal laser-scanning microscopy. The percentage of neurons and astrocytes was quantified by normalizing the total number of TUJ1+ (Neuron-specific class III β-tubulin) and GFAP+ (Glial fibrillary acidic protein) cells to the total number of Hoechst 33342-labeled cell nuclei. The protein and gene expression of Notch-Hes1 pathway components was examined via western blot analysis and real-time PCR. After 1 week of incubation, we found that AGE-bovine serum albumin (BSA) (400 μg/mL) induced the astrocytic differentiation of cultured neurospheres and inhibited neuronal formation. The expression of Notch-Hes1 pathway components was upregulated in the cells in the AGE-BSA culture medium. Immunoblot analysis indicated that shRNA silencing of Notch1 expression in NSCs significantly increases neurogenesis and suppresses astrocytic differentiation in NSCs incubated with AGE-BSA. AGEs promote the astrocytic differentiation of cultured neurospheres by inhibiting neurogenesis through the Notch-Hes1 pathway, providing a potential therapeutic target for hyperglycemia-related cognitive deficits. Full article
(This article belongs to the Special Issue Glycosylation and Glycoproteins)
Open AccessArticle A Novel Thylakoid Ascorbate Peroxidase from Jatrophacurcas Enhances Salt Tolerance in Transgenic Tobacco
Int. J. Mol. Sci. 2014, 15(1), 171-185; doi:10.3390/ijms15010171
Received: 16 October 2013 / Revised: 10 December 2013 / Accepted: 13 December 2013 / Published: 24 December 2013
Cited by 4 | PDF Full-text (2435 KB) | HTML Full-text | XML Full-text
Abstract
Ascorbate peroxidase (APX) plays an important role in the metabolism of hydrogen peroxide in higher plants. In the present study, a novel APX gene (JctAPX) was cloned from Jatropha curcas L. The deduced amino acid sequence was similar to that [...] Read more.
Ascorbate peroxidase (APX) plays an important role in the metabolism of hydrogen peroxide in higher plants. In the present study, a novel APX gene (JctAPX) was cloned from Jatropha curcas L. The deduced amino acid sequence was similar to that of APX of some other plant species. JctAPX has a chloroplast transit peptide and was localized to the chloroplasts by analysis with a JctAPX-green fluorescent protein (GFP) fusion protein. Quantitative polymerase chain reaction (qPCR) analysis showed that JctAPX was constitutively expressed in different tissues from J. curcas and was upregulated by NaCl stress. To characterize its function in salt tolerance, the construct p35S: JctAPX was created and successfully introduced into tobacco by Agrobacterium-mediated transformation. Compared with wild type (WT), the transgenic plants exhibited no morphological abnormalities in the no-stress condition. However, under 200 mM NaCl treatment, JctAPX over-expressing plants showed increased tolerance to salt during seedling establishment and growth. In addition, the transgenic lines showed higher chlorophyll content and APX activity, which resulted in lower H2O2 content than WT when subjected to 400 mM NaCl stress. These results suggest that the increased APX activity in the chloroplasts from transformed plants increased salt tolerance by enhancing reactive oxygen species (ROS)-scavenging capacity under short-term NaCl stress conditions. Full article
(This article belongs to the Special Issue Redox Signaling in Biology and Patho-Biology)
Open AccessArticle The Effect of 5'-Adenylic Acid on Hepatic Proteome of Mice Radiated by 60Co γ-ray
Int. J. Mol. Sci. 2014, 15(1), 186-202; doi:10.3390/ijms15010186
Received: 24 October 2013 / Revised: 15 December 2013 / Accepted: 18 December 2013 / Published: 24 December 2013
PDF Full-text (1014 KB) | HTML Full-text | XML Full-text
Abstract
Understanding the protection mechanism of 5'-AMP requires comprehensive knowledge of the proteins expressed during the period that the body is exposed to irradiation. Proteomics provides the tools for such analyses. Here, the experimental ICR mice were divided into three groups (normal group, [...] Read more.
Understanding the protection mechanism of 5'-AMP requires comprehensive knowledge of the proteins expressed during the period that the body is exposed to irradiation. Proteomics provides the tools for such analyses. Here, the experimental ICR mice were divided into three groups (normal group, model group and 5'-AMP + irradiation group). After different treatment, the hepatic total protein of each animal in three groups was separated by two-dimensional gel electrophoresis (2-DE). 2-DE analysis revealed fifty-eight protein spots were differentially expressed in comparison to three groups. From 58 protein spots, we selected nine spots to identify by MALDI-TOF-MS and received credible results. They were determined to be type I arginase, annexin A5, regucalcin, catalase, Tpm3 protein, Pdia4 protein, 14-3-3 protein epsilon, NAD-Malate dehydrogenase and heat shock protein 90. Considering the characteristic of these proteins, we proposed a possible protection pathway. Full article
(This article belongs to the collection Advances in Proteomic Research)
Figures

Open AccessArticle High-Level Expression of Pro-Form Lipase from Rhizopus oryzae in Pichia pastoris and Its Purification and Characterization
Int. J. Mol. Sci. 2014, 15(1), 203-217; doi:10.3390/ijms15010203
Received: 27 September 2013 / Revised: 11 December 2013 / Accepted: 13 December 2013 / Published: 24 December 2013
Cited by 8 | PDF Full-text (922 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A gene encoding Rhizopus oryzae lipase containing prosequence (ProROL) was cloned into the pPICZαA and electrotransformed into the Pichia pastoris X-33 strain. The lipase was functionally expressed and secreted in Pichia pastoris with a molecular weight of 35 kDa. The maximum lipase [...] Read more.
A gene encoding Rhizopus oryzae lipase containing prosequence (ProROL) was cloned into the pPICZαA and electrotransformed into the Pichia pastoris X-33 strain. The lipase was functionally expressed and secreted in Pichia pastoris with a molecular weight of 35 kDa. The maximum lipase activity of recombinant lipase (rProROL) was 21,000 U/mL, which was obtained in a fed-batch cultivation after 168 h induction with methanol in a 50-L bioreactor. After fermentation, the supernatant was concentrated by ultrafiltration with a 10 kDa cut off membrane and purified with ion exchange chromatography using SP Sepharose Fast Flow chromatography. The optimum pH and temperature of the rProROL were pH 9.0 and 40 °C, respectively. The lipase was stable from pH 4.0 to 9.0 and from 25 to 55 °C. The enzyme activity was enhanced by Ca2+ and inhibited by Hg2+ and Ag+. The lipase showed high activity toward triglyceride-Tripalmitin (C16:0) and triglyceride-Trilaurin (C12:0). Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle DNA Repair Gene XRCC4 Codon 247 Polymorphism Modified Diffusely Infiltrating Astrocytoma Risk and Prognosis
Int. J. Mol. Sci. 2014, 15(1), 250-260; doi:10.3390/ijms15010250
Received: 28 October 2013 / Revised: 1 December 2013 / Accepted: 23 December 2013 / Published: 27 December 2013
Cited by 3 | PDF Full-text (348 KB) | HTML Full-text | XML Full-text
Abstract
The DNA repair gene X-ray cross-complementary group 4 (XRCC4), an important caretaker of the overall genome stability, is thought to play a major role in human tumorigenesis. We investigated the association between an important polymorphic variant of this gene at codon 247 [...] Read more.
The DNA repair gene X-ray cross-complementary group 4 (XRCC4), an important caretaker of the overall genome stability, is thought to play a major role in human tumorigenesis. We investigated the association between an important polymorphic variant of this gene at codon 247 (rs373409) and diffusely infiltrating astrocytoma (DIA) risk and prognosis. This hospital-based case-control study investigated this association in the Guangxi population. In total, 242 cases with DIA and 358 age-, sex-, and race-matched healthy controls were genotyped using TaqMan-PCR technique. We found a significant difference in the frequency of XRCC4 genotypes between cases and controls. Compared with the homozygote of XRCC4 codon 247 Ala alleles (XRCC4-AA), the genotypes of XRCC4 codon 247 Ser alleles (namely XRCC4-AS or -SS) increased DIA risk (odds ratios [OR], 1.82 and 2.89, respectively). Furthermore, XRCC4 polymorphism was correlated with tumor dedifferentiation of DIA (r = 0.261, p < 0.01). Additionally, this polymorphism modified the overall survival of DIA patients (the median survival times were 26, 14, and 8 months for patients with XRCC4-AA, -AS, and -SS, respectively). Like tumor grade, XRCC4 codon 247 polymorphism was an independent prognostic factor influencing the survival of DIA. These results suggest that XRCC4 codon 247 polymorphism may be associated with DIA risk and prognosis among the Guangxi population. Full article
(This article belongs to the Section Molecular Diagnostics)
Open AccessArticle Development and Experimental Testing of an Optical Micro-Spectroscopic Technique Incorporating True Line-Scan Excitation
Int. J. Mol. Sci. 2014, 15(1), 261-276; doi:10.3390/ijms15010261
Received: 18 September 2013 / Revised: 15 December 2013 / Accepted: 23 December 2013 / Published: 27 December 2013
Cited by 7 | PDF Full-text (489 KB) | HTML Full-text | XML Full-text
Abstract
Multiphoton micro-spectroscopy, employing diffraction optics and electron-multiplying CCD (EMCCD) cameras, is a suitable method for determining protein complex stoichiometry, quaternary structure, and spatial distribution in living cells using Förster resonance energy transfer (FRET) imaging. The method provides highly resolved spectra of molecules [...] Read more.
Multiphoton micro-spectroscopy, employing diffraction optics and electron-multiplying CCD (EMCCD) cameras, is a suitable method for determining protein complex stoichiometry, quaternary structure, and spatial distribution in living cells using Förster resonance energy transfer (FRET) imaging. The method provides highly resolved spectra of molecules or molecular complexes at each image pixel, and it does so on a timescale shorter than that of molecular diffusion, which scrambles the spectral information. Acquisition of an entire spectrally resolved image, however, is slower than that of broad-bandwidth microscopes because it takes longer times to collect the same number of photons at each emission wavelength as in a broad bandwidth. Here, we demonstrate an optical micro-spectroscopic scheme that employs a laser beam shaped into a line to excite in parallel multiple sample voxels. The method presents dramatically increased sensitivity and/or acquisition speed and, at the same time, has excellent spatial and spectral resolution, similar to point-scan configurations. When applied to FRET imaging using an oligomeric FRET construct expressed in living cells and consisting of a FRET acceptor linked to three donors, the technique based on line-shaped excitation provides higher accuracy compared to the point-scan approach, and it reduces artifacts caused by photobleaching and other undesired photophysical effects. Full article
(This article belongs to the Special Issue Frontiers of Micro-Spectroscopy in Biological Applications)
Open AccessArticle Phenological, Nutritional and Molecular Diversity Assessment among 35 Introduced Lentil (Lens culinaris Medik.) Genotypes Grown in Saudi Arabia
Int. J. Mol. Sci. 2014, 15(1), 277-295; doi:10.3390/ijms15010277
Received: 17 September 2013 / Revised: 27 November 2013 / Accepted: 16 December 2013 / Published: 27 December 2013
Cited by 1 | PDF Full-text (268 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Morphological, nutritional and molecular analyses were carried out to assess genetic diversity among 35 introduced lentil genotypes (Lens culinaris Medik.). The genotypes exhibited significant differences for their field parameters and some of them showed noticeable superiority. The nutritional and proximate analysis [...] Read more.
Morphological, nutritional and molecular analyses were carried out to assess genetic diversity among 35 introduced lentil genotypes (Lens culinaris Medik.). The genotypes exhibited significant differences for their field parameters and some of them showed noticeable superiority. The nutritional and proximate analysis showed that some genotypes were excellent sources of proteins, essential amino acids, minerals, anti-oxidants, total phenolic contents (TPC) and total flavonoid contents (TFC) and hence, highlights lentil nutritional and medicinal potential. Sequence-related amplified polymorphism (SRAP) and amplified fragments length polymorphism (AFLP) markers were used to estimate the genetic variability at the molecular level. The existence of a considerable amount of genetic diversity among the tested lentil genotypes was also proven at the molecular level. A total of 2894 polymorphic SRAP and 1625 AFLP loci were successfully amplified using six SRAP and four AFLP primer pair combinations. Polymorphism information content (PIC) values for SRAP and AFLP markers were higher than 0.8, indicating the power and higher resolution of those marker systems in detecting molecular diversity. UPGMA (unweighted pair group method with arithmetic average) cluster analysis based on molecular data revealed large number of sub clusters among genotypes, indicating high diversity levels. The data presented here showed that FLIP2009-64L and FLIP2009-69L could be used as a significant source of yield, total protein, essential amino acids, and antioxidant properties. The results suggest potential lentil cultivation in the central region of Saudi Arabia for its nutritional and medicinal properties, as well as sustainable soil fertility crop. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle MiRNA-199a-3p Regulates C2C12 Myoblast Differentiation through IGF-1/AKT/mTOR Signal Pathway
Int. J. Mol. Sci. 2014, 15(1), 296-308; doi:10.3390/ijms15010296
Received: 15 November 2013 / Revised: 10 December 2013 / Accepted: 11 December 2013 / Published: 27 December 2013
Cited by 9 | PDF Full-text (1880 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
MicroRNAs constitute a class of ~22-nucleotide non-coding RNAs. They modulate gene expression by associating with the 3' untranslated regions (3' UTRs) of messenger RNAs (mRNAs). Although multiple miRNAs are known to be regulated during myoblast differentiation, their individual roles in muscle development [...] Read more.
MicroRNAs constitute a class of ~22-nucleotide non-coding RNAs. They modulate gene expression by associating with the 3' untranslated regions (3' UTRs) of messenger RNAs (mRNAs). Although multiple miRNAs are known to be regulated during myoblast differentiation, their individual roles in muscle development are still not fully understood. In this study, we showed that miR-199a-3p was highly expressed in skeletal muscle and was induced during C2C12 myoblasts differentiation. We also identified and confirmed several genes of the IGF-1/AKT/mTOR signal pathway, including IGF-1, mTOR, and RPS6KA6, as important cellular targets of miR-199a-3p in myoblasts. Overexpression of miR-199a-3p partially blocked C2C12 myoblast differentiation and the activation of AKT/mTOR signal pathway, while interference of miR-199a-3p by antisense oligonucleotides promoted C2C12 differentiation and myotube hypertrophy. Thus, our studies have established miR-199a-3p as a potential regulator of myogenesis through the suppression of IGF-1/AKT/mTOR signal pathway. Full article
Open AccessArticle Evaluation of Epirubicin in Thermogelling and Bioadhesive Liquid and Solid Suppository Formulations for Rectal Administration
Int. J. Mol. Sci. 2014, 15(1), 342-360; doi:10.3390/ijms15010342
Received: 18 August 2013 / Revised: 16 December 2013 / Accepted: 16 December 2013 / Published: 31 December 2013
PDF Full-text (1551 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Temperature sensitive Pluronic (Plu) and pH-sensitive polyacrylic acid (PAA) were successfully mixed in different ratios to form in situ gelling formulations for colon cancer therapy. The major formulations were prepared as the liquid and solid suppository dosage forms. Epirubicin (Epi) was chosen [...] Read more.
Temperature sensitive Pluronic (Plu) and pH-sensitive polyacrylic acid (PAA) were successfully mixed in different ratios to form in situ gelling formulations for colon cancer therapy. The major formulations were prepared as the liquid and solid suppository dosage forms. Epirubicin (Epi) was chosen as a model anticancer drug. In vitro characterization and in vivo pharmacokinetics and therapeutic efficacy of Epi in six Plu/PAA formulations were evaluated. Our in vitro data indicate that Epi in Plu 14%/PAA 0.75% of both solid and liquid suppositories possess significant cytotoxicity, strong bioadhesive force, long-term appropriate suppository base, sustained release, and high accumulation of Epi in rat rectums. These solid and liquid suppositories were retained in the upper rectum of Sprague-Dawley (SD) rats for at least 12 h. An in vivo pharmacokinetic study using SD rats showed that after rectal administration of solid and liquid suppositories, Epi had greater area under the curve and higher relative bioavailability than in a rectal solution. These solid and liquid suppositories exhibited remarkable inhibition on the tumor growth of CT26 bearing Balb/c mice in vivo. Our findings suggest that in situ thermogelling and mucoadhesive suppositories demonstrate a great potential as colon anticancer delivery systems for protracted release of chemotherapeutic agents. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Figures

Open AccessArticle Genetic Diversity and Population Structure of Siberian apricot (Prunus sibirica L.) in China
Int. J. Mol. Sci. 2014, 15(1), 377-400; doi:10.3390/ijms15010377
Received: 27 September 2013 / Revised: 5 December 2013 / Accepted: 5 December 2013 / Published: 31 December 2013
Cited by 5 | PDF Full-text (1843 KB) | HTML Full-text | XML Full-text
Abstract
The genetic diversity and population genetic structure of 252 accessions from 21 Prunus sibirica L. populations were investigated using 10 ISSR, SSR, and SRAP markers. The results suggest that the entire population has a relatively high level of genetic diversity, with populations [...] Read more.
The genetic diversity and population genetic structure of 252 accessions from 21 Prunus sibirica L. populations were investigated using 10 ISSR, SSR, and SRAP markers. The results suggest that the entire population has a relatively high level of genetic diversity, with populations HR and MY showing very high diversity. A low level of inter-population genetic differentiation and a high level of intra-population genetic differentiation was found, which is supported by a moderate level of gene flow, and largely attributable to the cross-pollination and self-incompatibility reproductive system. A STRUCTURE (model-based program) analysis revealed that the 21 populations can be divided into two main groups, mainly based on geographic differences and genetic exchanges. The entire wild Siberia apricot population in China could be divided into two subgroups, including 107 accessions in subgroup (SG) 1 and 147 accessions in SG 2. A Mantel test revealed a significant positive correlation between genetic and geographic distance matrices, and there was a very significant positive correlation among three marker datasets. Overall, we recommend a combination of conservation measures, with ex situ and in situ conservation that includes the construction of a core germplasm repository and the implement of in situ conservation for populations HR, MY, and ZY. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle miR-126 Functions as a Tumor Suppressor in Osteosarcoma by Targeting Sox2
Int. J. Mol. Sci. 2014, 15(1), 423-437; doi:10.3390/ijms15010423
Received: 7 October 2013 / Revised: 28 November 2013 / Accepted: 2 December 2013 / Published: 31 December 2013
Cited by 15 | PDF Full-text (1687 KB) | HTML Full-text | XML Full-text
Abstract
Osteosarcoma (OS) is the most common malignant bone tumor in children and young adults, the early symptoms and signs of which are non-specific. The discovery of microRNAs (miRNAs) provides a new avenue for the early diagnosis and treatment of OS. miR-126 has [...] Read more.
Osteosarcoma (OS) is the most common malignant bone tumor in children and young adults, the early symptoms and signs of which are non-specific. The discovery of microRNAs (miRNAs) provides a new avenue for the early diagnosis and treatment of OS. miR-126 has been reported to be highly expressed in vascularized tissues, and is recently widely studied in cancers. Herein, we explored the expression and significance of miR-126 in OS. Using TaqMan RT-PCR analysis, we analyzed the expression of miR-126 in 32 paired OS tumor tissues and 4 OS cell lines and found that miR-126 was consistently under-expressed in OS tissues and cell lines compared with normal bone tissues and normal osteoblast cells (NHOst), respectively. As miR-126 is significantly decreased in OS tissues and cell lines, we sought to compensate for its loss through exogenous transfection into MG-63 cells with a miR-126 mimic. Ectopic expression of miR-126 inhibited cell proliferation, migration and invasion, and induced apoptosis of MG-63 cells. Moreover, bioinformatic prediction suggested that the sex-determining region Y-box 2 (Sox2) is a target gene of miR-126. Using mRNA and protein expression analysis, luciferase assays and rescue assays, we demonstrate that restored expression of Sox2 dampened miR-126-mediated suppression of tumor progression, which suggests the important role of miR-126/Sox2 interaction in tumor progression. Taken together, our data indicate that miR-126 functions as a tumor suppressor in OS, which exerts its activity by suppressing the expression of Sox2. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Molecular Dynamics Simulation of the Crystallizable Fragment of IgG1—Insights for the Design of Fcabs
Int. J. Mol. Sci. 2014, 15(1), 438-455; doi:10.3390/ijms15010438
Received: 28 November 2013 / Revised: 19 December 2013 / Accepted: 27 December 2013 / Published: 2 January 2014
Cited by 4 | PDF Full-text (1697 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
An interesting format in the development of therapeutic monoclonal antibodies uses the crystallizable fragment of IgG1 as starting scaffold. Engineering of its structural loops allows generation of an antigen binding site. However, this might impair the molecule’s conformational stability, which can be [...] Read more.
An interesting format in the development of therapeutic monoclonal antibodies uses the crystallizable fragment of IgG1 as starting scaffold. Engineering of its structural loops allows generation of an antigen binding site. However, this might impair the molecule’s conformational stability, which can be overcome by introducing stabilizing point mutations in the CH3 domains. These point mutations often affect the stability and unfolding behavior of both the CH2 and CH3 domains. In order to understand this cross-talk, molecular dynamics simulations of the domains of the Fc fragment of human IgG1 are reported. The structure of human IgG1-Fc obtained from X-ray crystallography is used as a starting point for simulations of the wild-type protein at two different pH values. The stabilizing effect of a single point mutation in the CH3 domain as well as the impact of the hinge region and the glycan tree structure connected to the CH2 domains is investigated. Regions of high local flexibility were identified as potential sites for engineering antigen binding sites. Obtained data are discussed with respect to the available X-ray structure of IgG1-Fc, directed evolution approaches that screen for stability and use of the scaffold IgG1-Fc in the design of antigen binding Fc proteins. Full article
(This article belongs to the collection Proteins and Protein-Ligand Interactions)
Figures

Open AccessArticle Pharmacokinetic Comparison of Berberine in Rat Plasma after Oral Administration of Berberine Hydrochloride in Normal and Post Inflammation Irritable Bowel Syndrome Rats
Int. J. Mol. Sci. 2014, 15(1), 456-467; doi:10.3390/ijms15010456
Received: 12 November 2013 / Revised: 26 December 2013 / Accepted: 26 December 2013 / Published: 2 January 2014
Cited by 4 | PDF Full-text (378 KB) | HTML Full-text | XML Full-text
Abstract
In the present study, post inflammation irritable bowel syndrome (PI-IBS) rats were firstly established by intracolonic instillation of acetic acid with restraint stress. Then the pharmacokinetics of berberine in the rat plasma were compared after oral administration of berberine hydrochloride (25 mg/kg) [...] Read more.
In the present study, post inflammation irritable bowel syndrome (PI-IBS) rats were firstly established by intracolonic instillation of acetic acid with restraint stress. Then the pharmacokinetics of berberine in the rat plasma were compared after oral administration of berberine hydrochloride (25 mg/kg) to normal rats and PI-IBS rats. Quantification of berberine in the rat plasma was achieved by using a sensitive and rapid UPLC-MS/MS method. Plasma samples were collected at 15 different points in time and the pharmacokinetic parameters were analyzed by WinNonlin software. Compared with the normal group, area under the plasma concentration vs. time curve from zero to last sampling time (AUC0–t) and total body clearance (CL/F) in the model group significantly increased or decreased, (2039.49 ± 492.24 vs. 2763.43 ± 203.14; 4999.34 ± 1198.79 vs. 3270.57 ± 58.32) respectively. The results indicated that the pharmacokinetic process of berberine could be altered in PI-IBS pathological conditions. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle 1-(2,6-Dihydroxy-4-methoxyphenyl)-2-(4-hydroxyphenyl) Ethanone-Induced Cell Cycle Arrest in G1/G0 in HT-29 Cells Human Colon Adenocarcinoma Cells
Int. J. Mol. Sci. 2014, 15(1), 468-483; doi:10.3390/ijms15010468
Received: 12 October 2013 / Revised: 7 November 2013 / Accepted: 28 November 2013 / Published: 2 January 2014
Cited by 4 | PDF Full-text (980 KB) | HTML Full-text | XML Full-text
Abstract
1-(2,6-Dihydroxy-4-methoxyphenyl)-2-(4-hydroxyphenyl) ethanone (DMHE) was isolated from the ethyl acetate fraction of Phaleria macrocarpa (Scheff.) Boerl fruits and the structure confirmed by GC-MS (gas chromatography-mass spectrometry) and NMR (nuclear magnetic resonance) analysis. This compound was tested on the HT-29 human colon adenocarcinoma cell [...] Read more.
1-(2,6-Dihydroxy-4-methoxyphenyl)-2-(4-hydroxyphenyl) ethanone (DMHE) was isolated from the ethyl acetate fraction of Phaleria macrocarpa (Scheff.) Boerl fruits and the structure confirmed by GC-MS (gas chromatography-mass spectrometry) and NMR (nuclear magnetic resonance) analysis. This compound was tested on the HT-29 human colon adenocarcinoma cell line using MTT (method of transcriptional and translational) cell proliferation assay. The results of MTT assay showed that DMHE exhibited good cytotoxic effect on HT-29 cells in a dose- and time-dependent manner but no cytotoxic effect on the MRC-5 cell line after 72 h incubation. Morphological features of apoptotic cells upon treatment by DMHE, e.g., cell shrinkage and membrane blebbing, were examined by an inverted and phase microscope. Other features, such as chromatin condension and nuclear fragmentation were studied using acridine orange and propidium iodide staining under the fluorescence microscope. Future evidence of apoptosis/necrosis was provided by result fromannexin V-FITC/PI (fluorescein-isothiocyanate/propidium iodide) staining revealed the percentage of early apoptotic, late apoptotic, necrotic and live cells in a dose- and time-dependent manner using flow cytometry. Cell cycle analysis showed G0/G1 arrest in a time-dependent manner. A western blot analysis indicated that cell death might be associated with the up-regulation of the pro-apoptotic proteins Bax PUMA. However, the anit-apotptic proteins Bcl-2, Bcl-xL, and Mcl-1 were also found to increase in a time-dependent manner. The expression of the pro-apoptotic protein Bak was not observed. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle The Inhibitory Effect of Quercetin on Asymmetric Dimethylarginine-Induced Apoptosis Is Mediated by the Endoplasmic Reticulum Stress Pathway in Glomerular Endothelial Cells
Int. J. Mol. Sci. 2014, 15(1), 484-503; doi:10.3390/ijms15010484
Received: 10 October 2013 / Revised: 12 December 2013 / Accepted: 16 December 2013 / Published: 2 January 2014
Cited by 7 | PDF Full-text (3103 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Asymmetric dimethylarginine (ADMA) is considered an independent mortality and cardiovascular risk factor in chronic kidney disease (CKD) patients, and contributes to the development of renal fibrosis. Quercetin (QC), a natural component of foods, protects against renal injury. Here, we explored the possible [...] Read more.
Asymmetric dimethylarginine (ADMA) is considered an independent mortality and cardiovascular risk factor in chronic kidney disease (CKD) patients, and contributes to the development of renal fibrosis. Quercetin (QC), a natural component of foods, protects against renal injury. Here, we explored the possible mechanisms that are responsible for ADMA-induced renal fibrosis and the protective effect of QC. We found that ADMA treatment activated the endoplasmic reticulum (ER) stress sensor proteins phosphorylated protein kinase RNA-activated-like ER kinase (PERK) and inositol requiring-1α (IRE1), which correspondingly induced C/EBP homologous protein (CHOP) expression and phosphorylated c-Jun N-terminal kinase (JNK) phosphorylation in glomerular endothelial cells (GEnCs). Following this, ADMA promoted ER stress-induced apoptosis and resulted in transforming growth factor β (TGF-β) expression in GEnCs. SP600125, an inhibitor of JNK, and CHOP siRNA protected against ADMA-induced cell apoptosis and TGF-β expression. QC prevented ADMA-induced PERK and IRE1 apoptotic ER stress pathway activation. Also, ADMA-induced GEnCs apoptosis and TGF-β expression was reduced by QC. Overexpression of CHOP blocked QC-mediated protection from apoptosis in ER stressed cells. Overall, these observations indicate that ADMA may induce GEnCs apoptosis and TGF-β expression by targeting the PERK-CHOP and IRE1-JNK pathway. In addition, drugs such as QC targeting ER stress may hold great promise for the development of novel therapies against ADMA-induced renal fibrosis. Full article
(This article belongs to the collection Programmed Cell Death and Apoptosis)
Open AccessArticle Molecular Cloning, Bioinformatics Analysis and Expression of Insulin-Like Growth Factor 2 from Tianzhu White Yak, Bos grunniens
Int. J. Mol. Sci. 2014, 15(1), 504-524; doi:10.3390/ijms15010504
Received: 30 October 2013 / Revised: 16 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
Cited by 3 | PDF Full-text (1353 KB) | HTML Full-text | XML Full-text
Abstract
The IGF family is essential for normal embryonic and postnatal development and plays important roles in the immune system, myogenesis, bone metabolism and other physiological functions, which makes the study of its structure and biological characteristics important. Tianzhu white yak (Bos [...] Read more.
The IGF family is essential for normal embryonic and postnatal development and plays important roles in the immune system, myogenesis, bone metabolism and other physiological functions, which makes the study of its structure and biological characteristics important. Tianzhu white yak (Bos grunniens) domesticated under alpine hypoxia environments, is well adapted to survive and grow against severe hypoxia and cold temperatures for extended periods. In this study, a full coding sequence of the IGF2 gene of Tianzhu white yak was amplified by reverse transcription PCR and rapid-amplification of cDNA ends (RACE) for the first time. The cDNA sequence revealed an open reading frame of 450 nucleotides, encoding a protein with 179 amino acids. Its expression in different tissues was also studied by Real time PCR. Phylogenetic tree analysis indicated that yak IGF2 was similar to Bos taurus, and 3D structure showed high similarity with the human IGF2. The putative full CDS of yak IGF2 was amplified by PCR in five tissues, and cDNA sequence analysis showed high homology to bovine IGF2. Moreover the super secondary structure prediction showed a similar 3D structure with human IGF2. Its conservation in sequence and structure has facilitated research on IGF2 and its physiological function in yak. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Enhanced Antitumor Effects of Adenoviral-Mediated siRNA against GRP78 Gene on Adenosine-Induced Apoptosis in Human Hepatoma HepG2 Cells
Int. J. Mol. Sci. 2014, 15(1), 525-544; doi:10.3390/ijms15010525
Received: 13 November 2013 / Revised: 19 December 2013 / Accepted: 23 December 2013 / Published: 3 January 2014
Cited by 3 | PDF Full-text (2973 KB) | HTML Full-text | XML Full-text
Abstract
Our previous studies show that adenosine-induced apoptosis is involved in endoplasmic reticulum stress in HepG2 cells. In this study, we have investigated whether knockdown of GRP78 by short hairpin RNA (shRNA) increases the cytotoxic effects of adenosine in HepG2 cells. The adenovirus [...] Read more.
Our previous studies show that adenosine-induced apoptosis is involved in endoplasmic reticulum stress in HepG2 cells. In this study, we have investigated whether knockdown of GRP78 by short hairpin RNA (shRNA) increases the cytotoxic effects of adenosine in HepG2 cells. The adenovirus vector-delivered shRNA targeting GRP78 (Ad-shGRP78) was constructed and transfected into HepG2 cells. RT-PCR assay was used to determine RNA interference efficiency. Effects of knockdown of GRP78 on adenosine-induced cell viabilities, cell-cycle distribution and apoptosis, as well as relative protein expressions were determined by flow cytometry and/or Western blot analysis. The intracellular Ca2+ concentration was detected by laser scanning confocal microscope. Mitochondrial membrane potential (ΔΨm) was measured by a fluorospectrophotometer. The results revealed that GRP78 mRNA was significantly downregulated by Ad-shGRP78 transfection. Knockdown of GRP78 enhanced HepG2 cell sensitivity to adenosine by modulating G0/G1 arrest and stimulating Bax, Bak, m-calpain, caspase-4 and CHOP protein levels. Knockdown of GRP78 worsened cytosolic Ca2+ overload and ΔΨm loss. Knockdown of caspase-4 by shRNA decreased caspase-3 mRNA expression and cell apoptosis. These findings indicate that GRP 78 plays a protective role in ER stress-induced apoptosis and show that the combination of chemotherapy drug and RNA interference adenoviruses provides a new treatment strategy against malignant tumors. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Syk/JNK/AP-1 Signaling Pathway Mediates Interleukin-6-Promoted Cell Migration in Oral Squamous Cell Carcinoma
Int. J. Mol. Sci. 2014, 15(1), 545-559; doi:10.3390/ijms15010545
Received: 5 November 2013 / Revised: 20 December 2013 / Accepted: 23 December 2013 / Published: 6 January 2014
Cited by 11 | PDF Full-text (2268 KB) | HTML Full-text | XML Full-text
Abstract
Oral squamous cell carcinoma (OSCC) typically migrates and metastasizes. Interleukin-6 (IL-6) is a multifunctional cytokine associated with disease status and cancer outcomes. The effect of IL-6 on human OSCC cells, however, is unknown. Here, we showed that IL-6 increased cell migration and [...] Read more.
Oral squamous cell carcinoma (OSCC) typically migrates and metastasizes. Interleukin-6 (IL-6) is a multifunctional cytokine associated with disease status and cancer outcomes. The effect of IL-6 on human OSCC cells, however, is unknown. Here, we showed that IL-6 increased cell migration and Intercellular adhesion molecule-1 (ICAM-1) expression in OSCC cells. Pretreatment of OSCC cells with IL-6R monoclonal antibody (mAb) significantly abolished IL-6-induced cell migration and ICAM-1 expression. By contrast, IL-6-mediated cell motility and ICAM-1 upregulation were attenuated by the Syk and c-Jun N-terminal kinase (JNK) inhibitors. Stimulation of OSCC cells with IL-6 promoted Syk and JNK phosphorylation. Furthermore, IL-6 enhanced AP-1 activity, and the IL-6R mAb, Syk inhibitor, or JNK inhibitor all reduced IL-6-mediated c-Jun phosphorylation, c-Jun binding to the ICAM-1 promoter, and c-Jun translocation into the nucleus. Our results indicate that IL-6 enhances the migration of OSCC cells by increasing ICAM-1 expression through the IL-6R receptor and the Syk, JNK, and AP-1 signal transduction pathways. Full article
Open AccessArticle Combined MicroRNA-340 and ROCK1 mRNA Profiling Predicts Tumor Progression and Prognosis in Pediatric Osteosarcoma
Int. J. Mol. Sci. 2014, 15(1), 560-573; doi:10.3390/ijms15010560
Received: 29 October 2013 / Revised: 12 December 2013 / Accepted: 23 December 2013 / Published: 6 January 2014
Cited by 8 | PDF Full-text (404 KB) | HTML Full-text | XML Full-text
Abstract
To investigate the association of combined microRNA-340 (miR-340) and ROCK1 mRNA profiling with clinicopathologic features and prognosis in pediatric patients with osteosarcoma. Quantitative real-time reverse transcriptase-polymerase chain reaction analysis was performed to detect expression levels of miR-340 and ROCK1 mRNA in cancerous [...] Read more.
To investigate the association of combined microRNA-340 (miR-340) and ROCK1 mRNA profiling with clinicopathologic features and prognosis in pediatric patients with osteosarcoma. Quantitative real-time reverse transcriptase-polymerase chain reaction analysis was performed to detect expression levels of miR-340 and ROCK1 mRNA in cancerous and noncancerous bone tissues from 92 children treated for primary osteosarcomas. Compared with noncancerous bone tissues, the expression levels of miR-340 and ROCK1 mRNA were, respectively, downregulated and upregulated in osteosarcoma tissues (both p < 0.001), which was consistent with the results of in situ hybridization and immunohistochemistry analysis. The downregulation of miR-340 was negatively correlated with the upregulation of ROCK1 mRNA in osteosarcoma tissues (r = −0.78, p = 0.001). In addition, the combined miR-340 downregulation and ROCK1 upregulation (miR-340-low/ROCK1-high) occurred more frequently in osteosarcoma tissues with positive metastasis (p < 0.001) and poor response to pre-operative chemotherapy (p = 0.002). Moreover, miR-340-low/ROCK1-high expression was significantly associated with both shortest overall survival (p < 0.001) and progression-free survival (p < 0.001). Multivariate analysis further confirmed that miR-340-low/ROCK1-high expression was an independent prognostic factor of unfavorable survival in pediatric osteosarcoma (for overall survival: p = 0.006, for progression-free survival: p = 0.008). Our data offer convincing evidence, for the first time, that the combined miR-340 downregulation and ROCK1 upregulation may be linked to tumor progression and adverse prognosis in pediatric osteosarcoma. Full article
Open AccessArticle Atrazine Molecular Imprinted Polymers: Comparative Analysis by Far-Infrared and Ultraviolet Induced Polymerization
Int. J. Mol. Sci. 2014, 15(1), 574-587; doi:10.3390/ijms15010574
Received: 11 November 2013 / Revised: 26 December 2013 / Accepted: 30 December 2013 / Published: 6 January 2014
Cited by 10 | PDF Full-text (2935 KB) | HTML Full-text | XML Full-text
Abstract
Atrazine molecular imprinted polymers (MIPs) were comparatively synthesized using identical polymer formulation by far-infrared (FIR) radiation and ultraviolet (UV)-induced polymerization, respectively. Equilibrium binding experiments were carried out with the prepared MIPs; the results showed that MIPuv possessed specific binding to atrazine [...] Read more.
Atrazine molecular imprinted polymers (MIPs) were comparatively synthesized using identical polymer formulation by far-infrared (FIR) radiation and ultraviolet (UV)-induced polymerization, respectively. Equilibrium binding experiments were carried out with the prepared MIPs; the results showed that MIPuv possessed specific binding to atrazine compared with their MIPFIR radiation counterparts. Scatchard plot’s of both MIPs indicated that the affinities of the binding sites in MIPs are heterogeneous and can be approximated by two dissociation-constants corresponding to the high- and low-affinity binding sites. Moreover, several common pesticides including atrazine, cyromazine, metamitron, simazine, ametryn, terbutryn were tested to determine their specificity, similar imprinting factor (IF) and different selectivity index (SI) for both MIPs. Physical characterization of the polymers revealed that the different polymerization methods led to slight differences in polymer structures and performance by scanning electron microscope (SEM), Fourier transform infrared absorption (FT-IR), and mercury analyzer (MA). Finally, both MIPs were used as selective sorbents for solid phase extraction (SPE) of atrazine from lake water, followed by high performance liquid chromatography (HPLC) analysis. Compared with commercial C18 SPE sorbent (86.4%–94.8%), higher recoveries of atrazine in spiked lake water were obtained in the range of 90.1%–97.1% and 94.4%–101.9%, for both MIPs, respectively. Full article
Open AccessArticle Effects of Low Doses of Ionizing Radiation Exposures on Stress-Responsive Gene Expression in Human Embryonic Stem Cells
Int. J. Mol. Sci. 2014, 15(1), 588-604; doi:10.3390/ijms15010588
Received: 1 November 2013 / Revised: 25 December 2013 / Accepted: 26 December 2013 / Published: 6 January 2014
Cited by 7 | PDF Full-text (990 KB) | HTML Full-text | XML Full-text
Abstract
There is a great deal of uncertainty on how low (≤0.1 Gy) doses of ionizing radiation (IR) affect human cells, partly due to a lack of suitable experimental model systems for such studies. The uncertainties arising from low-dose IR human data undermine [...] Read more.
There is a great deal of uncertainty on how low (≤0.1 Gy) doses of ionizing radiation (IR) affect human cells, partly due to a lack of suitable experimental model systems for such studies. The uncertainties arising from low-dose IR human data undermine practical societal needs to predict health risks emerging from diagnostic medical tests’ radiation, natural background radiation, and environmental radiological accidents. To eliminate a variability associated with remarkable differences in radioresponses of hundreds of differentiated cell types, we established a novel, human embryonic stem cell (hESC)-based model to examine the radiobiological effects in human cells. Our aim is to comprehensively elucidate the gene expression changes in a panel of various hESC lines following low IR doses of 0.01; 0.05; 0.1 Gy; and, as a reference, relatively high dose of 1 Gy of IR. Here, we examined the dynamics of transcriptional changes of well-established IR-responsive set of genes, including CDKN1A, GADD45A, etc. at 2 and 16 h post-IR, representing “early” and “late” radioresponses of hESCs. Our findings suggest the temporal- and hESC line-dependence of stress gene radioresponses with no statistically significant evidence for a linear dose-response relationship within the lowest doses of IR exposures. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessArticle Hypoxic Conditioned Medium from Human Amniotic Fluid-Derived Mesenchymal Stem Cells Accelerates Skin Wound Healing through TGF-β/SMAD2 and PI3K/Akt Pathways
Int. J. Mol. Sci. 2014, 15(1), 605-628; doi:10.3390/ijms15010605
Received: 12 November 2013 / Revised: 21 December 2013 / Accepted: 2 January 2014 / Published: 6 January 2014
Cited by 22 | PDF Full-text (2169 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In a previous study, we isolated human amniotic fluid (AF)-derived mesenchymal stem cells (AF-MSCs) and utilized normoxic conditioned medium (AF-MSC-norCM) which has been shown to accelerate cutaneous wound healing. Because hypoxia enhances the wound healing function of mesenchymal stem cell-conditioned medium (MSC-CM), [...] Read more.
In a previous study, we isolated human amniotic fluid (AF)-derived mesenchymal stem cells (AF-MSCs) and utilized normoxic conditioned medium (AF-MSC-norCM) which has been shown to accelerate cutaneous wound healing. Because hypoxia enhances the wound healing function of mesenchymal stem cell-conditioned medium (MSC-CM), it is interesting to explore the mechanism responsible for the enhancement of wound healing function. In this work, hypoxia not only increased the proliferation of AF-MSCs but also maintained their constitutive characteristics (surface marker expression and differentiation potentials). Notably, more paracrine factors, VEGF and TGF-β1, were secreted into hypoxic conditioned medium from AF-MSCs (AF-MSC-hypoCM) compared to AF-MSC-norCM. Moreover, AF-MSC-hypoCM enhanced the proliferation and migration of human dermal fibroblasts in vitro, and wound closure in a skin injury model, as compared to AF-MSC-norCM. However, the enhancement of migration of fibroblasts accelerated by AF-MSC-hypoCM was inhibited by SB505124 and LY294002, inhibitors of TGF-β/SMAD2 and PI3K/AKT, suggesting that AF-MSC-hypoCM-enhanced wound healing is mediated by the activation of TGF-β/SMAD2 and PI3K/AKT. Therefore, AF-MSC-hypoCM enhances wound healing through the increase of hypoxia-induced paracrine factors via activation of TGF-β/SMAD2 and PI3K/AKT pathways. Full article
(This article belongs to the Special Issue Molecular Research of Epidermal Stem Cells)
Open AccessArticle Characterization of an Invertebrate-Type Dopamine Receptor of the American Cockroach, Periplaneta americana
Int. J. Mol. Sci. 2014, 15(1), 629-653; doi:10.3390/ijms15010629
Received: 29 November 2013 / Revised: 20 December 2013 / Accepted: 24 December 2013 / Published: 6 January 2014
Cited by 3 | PDF Full-text (1446 KB) | HTML Full-text | XML Full-text
Abstract
We have isolated a cDNA coding for a putative invertebrate-type dopamine receptor (Peadop2) from P. americana brain by using a PCR-based strategy. The mRNA is present in samples from brain and salivary glands. We analyzed the distribution of the PeaDOP2 [...] Read more.
We have isolated a cDNA coding for a putative invertebrate-type dopamine receptor (Peadop2) from P. americana brain by using a PCR-based strategy. The mRNA is present in samples from brain and salivary glands. We analyzed the distribution of the PeaDOP2 receptor protein with specific affinity-purified polyclonal antibodies. On Western blots, PeaDOP2 was detected in protein samples from brain, subesophageal ganglion, thoracic ganglia, and salivary glands. In immunocytochemical experiments, we detected PeaDOP2 in neurons with their somata being located at the anterior edge of the medulla bilaterally innervating the optic lobes and projecting to the ventro-lateral protocerebrum. In order to determine the functional and pharmacological properties of the cloned receptor, we generated a cell line constitutively expressing PeaDOP2. Activation of PeaDOP2-expressing cells with dopamine induced an increase in intracellular cAMP. In contrast, a C-terminally truncated splice variant of this receptor did not exhibit any functional property by itself. The molecular and pharmacological characterization of the first dopamine receptor from P. americana provides the basis for forthcoming studies focusing on the significance of the dopaminergic system in cockroach behavior and physiology. Full article
(This article belongs to the collection G Protein-Coupled Receptor Signaling and Regulation)
Open AccessArticle Association of Polymorphisms of Exon 2 of the Growth Hormone Gene with Production Performance in Huoyan Goose
Int. J. Mol. Sci. 2014, 15(1), 670-683; doi:10.3390/ijms15010670
Received: 1 October 2013 / Revised: 25 December 2013 / Accepted: 27 December 2013 / Published: 7 January 2014
Cited by 2 | PDF Full-text (736 KB) | HTML Full-text | XML Full-text
Abstract
Primers based on the cDNA sequence of the goose growth hormone (GH) gene in GenBank were designed to amplify exon 2 of the GH gene in Huoyan goose. A total of 552 individuals were brooded in one batch and raised in Liaoning [...] Read more.
Primers based on the cDNA sequence of the goose growth hormone (GH) gene in GenBank were designed to amplify exon 2 of the GH gene in Huoyan goose. A total of 552 individuals were brooded in one batch and raised in Liaoning and Jiangsu Provinces, China. Single nucleotide polymorphisms (SNPs) of exon 2 in the GH gene were detected by the polymerase chain reaction (single strand conformation polymorphism method). Homozygotes were subsequently cloned, sequenced and analyzed. Two SNP mutations were detected, and 10 genotypes (referred to as AA, BB, CC, DD, AB, AC, AD, BC, BD and CD) were obtained. Allele D was predominant, and the frequencies of the 10 genotypes fit the Hardy-Weinberg equilibrium in the male, female and whole populations according to the chi-square test. Based on SNP types, the 10 genotypes were combined into three main genotypes. Multiple comparisons were carried out between different genotypes and production traits when the geese were 10 weeks old. Some indices of production performance were significantly (p < 0.05) associated with the genotype. Particularly, geese with genotype AB or BB were highly productive. Thus, these genotypes may serve as selection markers for production traits in Huoyan geese. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Analysis of the rs10046 Polymorphism of Aromatase (CYP19) in Premenopausal Onset of Human Breast Cancer
Int. J. Mol. Sci. 2014, 15(1), 712-724; doi:10.3390/ijms15010712
Received: 5 December 2013 / Revised: 23 December 2013 / Accepted: 25 December 2013 / Published: 7 January 2014
Cited by 10 | PDF Full-text (303 KB) | HTML Full-text | XML Full-text
Abstract
The CYP19 gene encodes aromatase, an enzyme catalyzing the conversion of androgens to estrogens. Studies analyzing associations between single nucleotide polymorphisms in CYP19 and breast cancer risk have shown inconsistent results. The rs10046 polymorphism is located in the 3' untranslated region [...] Read more.
The CYP19 gene encodes aromatase, an enzyme catalyzing the conversion of androgens to estrogens. Studies analyzing associations between single nucleotide polymorphisms in CYP19 and breast cancer risk have shown inconsistent results. The rs10046 polymorphism is located in the 3' untranslated region of the CYP19 gene, but the influence of this polymorphism on breast cancer risk is unclear. In this study, we investigated the impact of rs10046 SNP on breast cancer risk, age at onset and association with clinical characteristics in an Austrian population of 274 breast cancer patients and 253 controls. The results show that a significantly increased fraction of patients with the TT genotype of rs10046 develop breast cancer under the age of 50 (41.8% of TT patients, compared to 26.6% of C carriers; p = 0.018, Chi-square test). No rs10046 genotypes were significantly associated with increased breast cancer risk or patient characteristics other than age at onset. These results suggest that the rs10046 polymorphism in the CYP19 gene may have an effect on breast cancer susceptibility at an age under 50 in the investigated population. Full article
(This article belongs to the collection Human Single Nucleotide Polymorphisms and Disease Diagnostics)
Open AccessArticle An Improved MLVF Method and Its Comparison with Traditional MLVF, spa Typing, MLST/SCCmec and PFGE for the Typing of Methicillin-Resistant Staphylococcus aureus
Int. J. Mol. Sci. 2014, 15(1), 725-742; doi:10.3390/ijms15010725
Received: 15 November 2013 / Revised: 12 December 2013 / Accepted: 20 December 2013 / Published: 8 January 2014
Cited by 3 | PDF Full-text (733 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has become an important nosocomial pathogen, causing considerable morbidity and mortality. During the last 20 years, a variety of genotyping methods have been introduced for screening the prevalence of MRSA. In this study, we developed and evaluated an [...] Read more.
Methicillin-resistant Staphylococcus aureus (MRSA) has become an important nosocomial pathogen, causing considerable morbidity and mortality. During the last 20 years, a variety of genotyping methods have been introduced for screening the prevalence of MRSA. In this study, we developed and evaluated an improved approach capillary gel electrophoresis based multilocus variable-number tandem-repeat fingerprinting (CGE/MLVF) for rapid MRSA typing. A total of 42 well-characterized strains and 116 non-repetitive clinical MRSA isolates collected from six hospitals in northeast China between 2009 and 2010 were tested. The results obtained by CGE/MLVF against clinical isolates were compared with traditional MLVF, spa typing, Multilocus sequence typing/ staphylococcal cassette chromosome mec (MLST/SCCmec) and pulse field gel electrophoresis (PFGE). The discriminatory power estimated by Simpson’s index of diversity was 0.855 (28 types), 0.855 (28 patterns), 0.623 (11 types), 0.517 (8 types) and 0.854 (28 patterns) for CGE/MLVF, traditional MLVF, spa typing, MLST/SCCmec and PFGE, respectively. All methods tested showed a satisfied concordance in clonal complex level calculated by adjusted Rand’s coefficient. CGE/MLVF showed better reproducibility and accuracy than traditional MLVF and PFGE methods. In addition, the CGE/MLVF has potential to produce portable results. In conclusion, CGE/MLVF is a rapid and easy to use MRSA typing method with lower cost, good reproducibility and high discriminatory power for monitoring the outbreak and clonal spread of MRSA isolates. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Figures

Open AccessArticle Modulation of Cyclins, p53 and Mitogen-Activated Protein Kinases Signaling in Breast Cancer Cell Lines by 4-(3,4,5-Trimethoxyphenoxy)benzoic Acid
Int. J. Mol. Sci. 2014, 15(1), 743-757; doi:10.3390/ijms15010743
Received: 19 November 2013 / Revised: 23 December 2013 / Accepted: 30 December 2013 / Published: 8 January 2014
Cited by 2 | PDF Full-text (2121 KB) | HTML Full-text | XML Full-text
Abstract
Despite the advances in cancer therapy and early detection, breast cancer remains a leading cause of cancer-related deaths among females worldwide. The aim of the current study was to investigate the antitumor activity of a novel compound, 4-(3,4,5-trimethoxyphenoxy)benzoic acid (TMPBA) and its [...] Read more.
Despite the advances in cancer therapy and early detection, breast cancer remains a leading cause of cancer-related deaths among females worldwide. The aim of the current study was to investigate the antitumor activity of a novel compound, 4-(3,4,5-trimethoxyphenoxy)benzoic acid (TMPBA) and its mechanism of action, in breast cancer. Results indicated the relatively high sensitivity of human breast cancer cell-7 and MDA-468 cells towards TMPBA with IC50 values of 5.9 and 7.9 µM, respectively compared to hepatocarcinoma cell line Huh-7, hepatocarcinoma cell line HepG2, and cervical cancer cell line Hela cells. Mechanistically, TMPBA induced apoptotic cell death in MCF-7 cells as indicated by 4',6-diamidino-2-phenylindole (DAPI) nuclear staining, cell cycle analysis and the activation of caspase-3. Western blot analysis revealed the ability of TMPBA to target pathways mediated by mitogen-activated protein (MAP) kinases, 5' adenosine monophosphate-activated protein kinase (AMPK), and p53, of which the concerted action underlined its antitumor efficacy. In addition, TMPBA induced alteration of cyclin proteins’ expression and consequently modulated the cell cycle. Taken together, the current study underscores evidence that TMPBA induces apoptosis in breast cancer cells via the modulation of cyclins and p53 expression as well as the modulation of AMPK and mitogen-activated protein kinases (MAPK) signaling. These findings support TMPBA’s clinical promise as a potential candidate for breast cancer therapy. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Increased Exosomal MicroRNA-21 and MicroRNA-146a Levels in the Cervicovaginal Lavage Specimens of Patients with Cervical Cancer
Int. J. Mol. Sci. 2014, 15(1), 758-773; doi:10.3390/ijms15010758
Received: 8 November 2013 / Revised: 12 December 2013 / Accepted: 16 December 2013 / Published: 8 January 2014
Cited by 23 | PDF Full-text (1712 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Well-run screening programs for cervical cancer in the population at risk have been shown to result in a sharp decrease in the incidence and mortality of cervical cancer in a number of large populations. Expression patterns of a recently identified biomarker family, [...] Read more.
Well-run screening programs for cervical cancer in the population at risk have been shown to result in a sharp decrease in the incidence and mortality of cervical cancer in a number of large populations. Expression patterns of a recently identified biomarker family, microRNA, appear to be characteristic of tumor type and developmental origin. Several tumors have been reported to actively release exosomes carrying microRNAs. The present study has determined the association of microRNAs with cervical cancer-derived exosomes. The cervical cancer-derived exosomes were enriched in the cervicovaginal lavages specimens and the abundance of exosomes and exosomal microRNAs was detected by electron microscopy, western blot analysis, RT-qPCR and microRNA target reporter vector. The microRNA-21 and microRNA-146a, which were up-regulated in cervical cancer patients, were associated with the high levels of cervical cancer-derived exosomes. In conclusion, we demonstrated the abundance of exosomes in the cervicovaginal lavage specimens of women with cervical cancer. Furthermore, our results indicated that abnormally high levels of microRNA-21 and microRNA-146a existed in the cervical cancer-derived exosomes and the two microRNAs were functional in 293T cells. Full article
(This article belongs to the Special Issue Advances in Cancer Diagnosis)
Open AccessArticle Dual Drug Release Electrospun Core-Shell Nanofibers with Tunable Dose in the Second Phase
Int. J. Mol. Sci. 2014, 15(1), 774-786; doi:10.3390/ijms15010774
Received: 19 November 2013 / Revised: 26 December 2013 / Accepted: 27 December 2013 / Published: 8 January 2014
Cited by 10 | PDF Full-text (1124 KB) | HTML Full-text | XML Full-text
Abstract
This study reports a new type of drug-loaded core-shell nanofibers capable of providing dual controlled release with tunable dose in the second phase. The core-shell nanofibers were fabricated through a modified coaxial electrospinning using a Teflon-coated concentric spinneret. Poly(vinyl pyrrolidone) and ethyl [...] Read more.
This study reports a new type of drug-loaded core-shell nanofibers capable of providing dual controlled release with tunable dose in the second phase. The core-shell nanofibers were fabricated through a modified coaxial electrospinning using a Teflon-coated concentric spinneret. Poly(vinyl pyrrolidone) and ethyl cellulose were used as the shell and core polymer matrices respectively, and the content of active ingredient acetaminophen (APAP) in the core was programmed. The Teflon-coated concentric spinneret may facilitate the efficacious and stable preparation of core-shell nanofibers through the modified coaxial electrospinning, where the core fluids were electrospinnable and the shell fluid had no electrospinnability. The resultant nanofibers had linear morphologies and clear core-shell structures, as observed by the scanning and transmission electron microscopic images. APAP was amorphously distributed in the shell and core polymer matrices due to the favorite second-order interactions, as indicated by the X-ray diffraction and FTIR spectroscopic tests. The results from the in vitro dissolution tests demonstrated that the core-shell nanofibers were able to furnish the desired dual drug controlled-release profiles with a tunable drug release amount in the second phase. The modified coaxial electrospinning is a useful tool to generate nanostructures with a tailored components and compositions in their different parts, and thus to realize the desired functional performances. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Figures

Open AccessArticle Structural Characterization of a Water-Soluble Polysaccharide from the Fruiting Bodies of Agaricus bisporus
Int. J. Mol. Sci. 2014, 15(1), 787-797; doi:10.3390/ijms15010787
Received: 22 November 2013 / Revised: 12 December 2013 / Accepted: 17 December 2013 / Published: 8 January 2014
PDF Full-text (360 KB) | HTML Full-text | XML Full-text
Abstract
An edible fungal polysaccharide termed as ABP was obtained by extraction with hot water, and followed successive chromatographic purification using DEAE-Sepharose Fast Flow column and Sephacryl S-300 High-Resolution column. A symmetrical peak was obtained on high-performance size-exclusion chromatography with an average molecular [...] Read more.
An edible fungal polysaccharide termed as ABP was obtained by extraction with hot water, and followed successive chromatographic purification using DEAE-Sepharose Fast Flow column and Sephacryl S-300 High-Resolution column. A symmetrical peak was obtained on high-performance size-exclusion chromatography with an average molecular weight of 5.17 × 104 Da, which was named ABP, and its main components were D-glucose and D-mannose. Based on the study of methylation analysis, along with FT-IR, GC, GC-MS, 1D 1H and 13C NMR and 2D NMR (H-HCOSY, TOCSY, HMQC, and NOESY), its chemical structure was featured with a repeating unit (1→6) linking β-D-Glcp as the main backbone with (1→4)-linked α-D-Manp units. The structure of the mainly repeating units of ABP was established as: [PLEASE CHECK FORMULA IN THE PDF] Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Towards Automated Binding Affinity Prediction Using an Iterative Linear Interaction Energy Approach
Int. J. Mol. Sci. 2014, 15(1), 798-816; doi:10.3390/ijms15010798
Received: 14 November 2013 / Revised: 17 December 2013 / Accepted: 23 December 2013 / Published: 9 January 2014
Cited by 4 | PDF Full-text (6746 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Binding affinity prediction of potential drugs to target and off-target proteins is an essential asset in drug development. These predictions require the calculation of binding free energies. In such calculations, it is a major challenge to properly account for both the dynamic [...] Read more.
Binding affinity prediction of potential drugs to target and off-target proteins is an essential asset in drug development. These predictions require the calculation of binding free energies. In such calculations, it is a major challenge to properly account for both the dynamic nature of the protein and the possible variety of ligand-binding orientations, while keeping computational costs tractable. Recently, an iterative Linear Interaction Energy (LIE) approach was introduced, in which results from multiple simulations of a protein-ligand complex are combined into a single binding free energy using a Boltzmann weighting-based scheme. This method was shown to reach experimental accuracy for flexible proteins while retaining the computational efficiency of the general LIE approach. Here, we show that the iterative LIE approach can be used to predict binding affinities in an automated way. A workflow was designed using preselected protein conformations, automated ligand docking and clustering, and a (semi-)automated molecular dynamics simulation setup. We show that using this workflow, binding affinities of aryloxypropanolamines to the malleable Cytochrome P450 2D6 enzyme can be predicted without a priori knowledge of dominant protein-ligand conformations. In addition, we provide an outlook for an approach to assess the quality of the LIE predictions, based on simulation outcomes only. Full article
(This article belongs to the Special Issue Xenobiotic Metabolism)
Figures

Open AccessArticle Increased Preventive Effect on Colon Carcinogenesis by Use of Resistant Starch (RS3) as the Carrier for Polysaccharide of Larimichthys Crocea Swimming Bladder
Int. J. Mol. Sci. 2014, 15(1), 817-829; doi:10.3390/ijms15010817
Received: 1 December 2013 / Revised: 20 December 2013 / Accepted: 30 December 2013 / Published: 9 January 2014
Cited by 7 | PDF Full-text (1002 KB) | HTML Full-text | XML Full-text
Abstract
The preventive effect of polysaccharide of Larimichthys crocea swimming bladder (PLCSB) and the increase of this effect by use of resistant starch (RS3) as the carrier for PLCSB on azoxymethane (AOM) and dextran sulfate sodium (DSS)-inducing colon carcinogenesis in C57BL/6 mice has [...] Read more.
The preventive effect of polysaccharide of Larimichthys crocea swimming bladder (PLCSB) and the increase of this effect by use of resistant starch (RS3) as the carrier for PLCSB on azoxymethane (AOM) and dextran sulfate sodium (DSS)-inducing colon carcinogenesis in C57BL/6 mice has been studied. RS3 microspheres carrying PLCSB (RS3 + PLCSB) were produced and evaluated as a potentially improved colon carcinogenesis therapy for this study. The body weight, colon length, and colon weight of mice were determined, and colonic tissues were histologically observed. The serum levels of proinflammatory cytokines and the inflammation and apoptosis-related genes in colonic tissue were also tested. The PLCSB or RS3 + PLCSB significantly suppressed AOM and DSS-induced body weight loss, colon length shortening and decreased the colon weight to length ratio. PLCSB or RS3 + PLCSB reduced the levels of the serum pro-inflammatory cytokines IL-6, IL-12, TNF-α, and IFN-γ to a greater extent compared with the control mice, and the levels of RS3 + PLCSB were more close to the normal mice than PLCSB treated mice. Histopathological examination of sections of colon tissues showed that the RS3 + PLCSB group recovered well from colon carcinogenesis; however, the tissue sections of the stachyose + starch could reduce the necrosis degree. PLCSB significantly induced apoptosis in tissues of mice (p < 0.05) by up-regulating Bax, caspase-3, and caspase-9, and down-regulating Bcl-2. The expression of genes associated with inflammation-related NF-κB, iNOS, and COX-2 genes, was significantly down-regulated, and IκB-α was up-regulated (p < 0.05). These results suggest that PLCSB is a potent preventive against in vivo colon carcinogenesis and that PLCSB with an RS3 carrier could increase the preventative effect in mice. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Conserved miRNAs and Their Response to Salt Stress in Wild Eggplant Solanum linnaeanum Roots
Int. J. Mol. Sci. 2014, 15(1), 839-849; doi:10.3390/ijms15010839
Received: 12 November 2013 / Revised: 19 November 2013 / Accepted: 30 December 2013 / Published: 9 January 2014
Cited by 11 | PDF Full-text (454 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The Solanaceae family includes some important vegetable crops, and they often suffer from salinity stress. Some miRNAs have been identified to regulate gene expression in plant response to salt stress; however, little is known about the involvement of miRNAs in Solanaceae species. [...] Read more.
The Solanaceae family includes some important vegetable crops, and they often suffer from salinity stress. Some miRNAs have been identified to regulate gene expression in plant response to salt stress; however, little is known about the involvement of miRNAs in Solanaceae species. To identify salt-responsive miRNAs, high-throughput sequencing was used to sequence libraries constructed from roots of the salt tolerant species, Solanum linnaeanum, treated with and without NaCl. The sequencing identified 98 conserved miRNAs corresponding to 37 families, and some of these miRNAs and their expression were verified by quantitative real-time PCR. Under the salt stress, 11 of the miRNAs were down-regulated, and 3 of the miRNAs were up-regulated. Potential targets of the salt-responsive miRNAs were predicted to be involved in diverse cellular processes in plants. This investigation provides valuable information for functional characterization of miRNAs in S. linnaeanum, and would be useful for developing strategies for the genetic improvement of the Solanaceae crops. Full article
(This article belongs to the Special Issue Regulation by non-coding RNAs 2013)
Open AccessArticle Changing Microspatial Patterns of Sulfate-Reducing Microorganisms (SRM) during Cycling of Marine Stromatolite Mats
Int. J. Mol. Sci. 2014, 15(1), 850-877; doi:10.3390/ijms15010850
Received: 1 November 2013 / Revised: 20 December 2013 / Accepted: 30 December 2013 / Published: 9 January 2014
Cited by 3 | PDF Full-text (1101 KB) | HTML Full-text | XML Full-text
Abstract
Microspatial arrangements of sulfate-reducing microorganisms (SRM) in surface microbial mats (~1.5 mm) forming open marine stromatolites were investigated. Previous research revealed three different mat types associated with these stromatolites, each with a unique petrographic signature. Here we focused on comparing “non-lithifying” (Type-1) [...] Read more.
Microspatial arrangements of sulfate-reducing microorganisms (SRM) in surface microbial mats (~1.5 mm) forming open marine stromatolites were investigated. Previous research revealed three different mat types associated with these stromatolites, each with a unique petrographic signature. Here we focused on comparing “non-lithifying” (Type-1) and “lithifying” (Type-2) mats. Our results revealed three major trends: (1) Molecular typing using the dsrA probe revealed a shift in the SRM community composition between Type-1 and Type-2 mats. Fluorescence in-situ hybridization (FISH) coupled to confocal scanning-laser microscopy (CSLM)-based image analyses, and 35SO42−-silver foil patterns showed that SRM were present in surfaces of both mat types, but in significantly (p < 0.05) higher abundances in Type-2 mats. Over 85% of SRM cells in the top 0.5 mm of Type-2 mats were contained in a dense 130 µm thick horizontal layer comprised of clusters of varying sizes; (2) Microspatial mapping revealed that locations of SRM and CaCO3 precipitation were significantly correlated (p < 0.05); (3) Extracts from Type-2 mats contained acylhomoserine-lactones (C4- ,C6- ,oxo-C6,C7- ,C8- ,C10- ,C12- , C14-AHLs) involved in cell-cell communication. Similar AHLs were produced by SRM mat-isolates. These trends suggest that development of a microspatially-organized SRM community is closely-associated with the hallmark transition of stromatolite surface mats from a non-lithifying to a lithifying state. Full article
(This article belongs to the Special Issue Biofilms: Extracellular Bastions of Bacteria) Print Edition available
Open AccessArticle Effect of Nanoparticles Exposure on Fractional Exhaled Nitric Oxide (FENO) in Workers Exposed to Nanomaterials
Int. J. Mol. Sci. 2014, 15(1), 878-894; doi:10.3390/ijms15010878
Received: 11 December 2013 / Revised: 26 December 2013 / Accepted: 3 January 2014 / Published: 9 January 2014
Cited by 9 | PDF Full-text (320 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Fractional exhaled nitric oxide (FENO) measurement is a useful diagnostic test of airway inflammation. However, there have been few studies of FENO in workers exposed to nanomaterials. The purpose of this study was to examine the effect of nanoparticle (NP) exposure on [...] Read more.
Fractional exhaled nitric oxide (FENO) measurement is a useful diagnostic test of airway inflammation. However, there have been few studies of FENO in workers exposed to nanomaterials. The purpose of this study was to examine the effect of nanoparticle (NP) exposure on FENO and to assess whether the FENO is increased in workers exposed to nanomaterials (NM). In this study, both exposed workers and non-exposed controls were recruited from NM handling plants in Taiwan. A total of 437 subjects (exposed group = 241, non-exposed group = 196) completed the FENO and spirometric measurements from 2009–2011. The authors used a control-banding (CB) matrix to categorize the risk level of each participant. In a multivariate linear regression analysis, this study found a significant association between risk level 2 of NP exposure and FENO. Furthermore, asthma, allergic rhinitis, peak expiratory flow rate (PEFR), and NF-κB were also significantly associated with FENO. When the multivariate logistic regression model was adjusted for confounders, nano-TiO2 in all of the NM exposed categories had a significantly increased risk in FENO > 35 ppb. This study found associations between the risk level of NP exposure and FENO (particularly noteworthy for Nano-TiO2). Monitoring FENO in the lung could open up a window into the role nitric oxide (NO) may play in pathogenesis. Full article
(This article belongs to the Special Issue Nanotoxicology and Lung Diseases)
Open AccessCommunication Luteolin Reduces Alzheimer’s Disease Pathologies Induced by Traumatic Brain Injury
Int. J. Mol. Sci. 2014, 15(1), 895-904; doi:10.3390/ijms15010895
Received: 29 October 2013 / Revised: 3 January 2014 / Accepted: 6 January 2014 / Published: 9 January 2014
Cited by 12 | PDF Full-text (357 KB) | HTML Full-text | XML Full-text
Abstract
Traumatic brain injury (TBI) occurs in response to an acute insult to the head and is recognized as a major risk factor for Alzheimer’s disease (AD). Indeed, recent studies have suggested a pathological overlap between TBI and AD, with both conditions exhibiting [...] Read more.
Traumatic brain injury (TBI) occurs in response to an acute insult to the head and is recognized as a major risk factor for Alzheimer’s disease (AD). Indeed, recent studies have suggested a pathological overlap between TBI and AD, with both conditions exhibiting amyloid-beta (Aβ) deposits, tauopathy, and neuroinflammation. Additional studies involving animal models of AD indicate that some AD-related genotypic determinants may be critical factors enhancing temporal and phenotypic symptoms of TBI. Thus in the present study, we examined sub-acute effects of moderate TBI delivered by a gas-driven shock tube device in Aβ depositing Tg2576 mice. Three days later, significant increases in b-amyloid deposition, glycogen synthase-3 (GSK-3) activation, phospho-tau, and pro-inflammatory cytokines were observed. Importantly, peripheral treatment with the naturally occurring flavonoid, luteolin, significantly abolished these accelerated pathologies. This study lays the groundwork for a safe and natural compound that could prevent or treat TBI with minimal or no deleterious side effects in combat personnel and others at risk or who have experienced TBI. Full article
(This article belongs to the Special Issue Pathology and Treatment of Central Nervous System Diseases)
Open AccessArticle Genomic and Phenotypic Alterations of the Neuronal-Like Cells Derived from Human Embryonal Carcinoma Stem Cells (NT2) Caused by Exposure to Organophosphorus Compounds Paraoxon and Mipafox
Int. J. Mol. Sci. 2014, 15(1), 905-926; doi:10.3390/ijms15010905
Received: 14 October 2013 / Revised: 8 December 2013 / Accepted: 17 December 2013 / Published: 9 January 2014
Cited by 7 | PDF Full-text (780 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Historically, only few chemicals have been identified as neurodevelopmental toxicants, however, concern remains, and has recently increased, based upon the association between chemical exposures and increased developmental disorders. Diminution in motor speed and latency has been reported in preschool children from agricultural [...] Read more.
Historically, only few chemicals have been identified as neurodevelopmental toxicants, however, concern remains, and has recently increased, based upon the association between chemical exposures and increased developmental disorders. Diminution in motor speed and latency has been reported in preschool children from agricultural communities. Organophosphorus compounds (OPs) are pesticides due to their acute insecticidal effects mediated by the inhibition of acetylcholinesterase, although other esterases as neuropathy target esterase (NTE) can also be inhibited. Other neurological and neurodevelopmental toxic effects with unknown targets have been reported after chronic exposure to OPs in vivo. We studied the initial stages of retinoic acid acid-triggered differentiation of pluripotent cells towards neural progenitors derived from human embryonal carcinoma stem cells to determine if neuropathic OP, mipafox, and non-neuropathic OP, paraoxon, are able to alter differentiation of neural precursor cells in vitro. Exposure to 1 µM paraoxon (non-cytotoxic concentrations) altered the expression of different genes involved in signaling pathways related to chromatin assembly and nucleosome integrity. Conversely, exposure to 5 µM mipafox, a known inhibitor of NTE activity, showed no significant changes on gene expression. We conclude that 1 µM paraoxon could affect the initial stage of in vitro neurodifferentiation possibly due to a teratogenic effect, while the absence of transcriptional alterations by mipafox exposure did not allow us to conclude a possible effect on neurodifferentiation pathways at the tested concentration. Full article
(This article belongs to the collection Molecular Research in Neurotoxicology)
Open AccessArticle Purification and Characterization of Iso-Ribonucleases from a Novel Thermophilic Fungus
Int. J. Mol. Sci. 2014, 15(1), 944-957; doi:10.3390/ijms15010944
Received: 10 December 2013 / Revised: 31 December 2013 / Accepted: 2 January 2014 / Published: 10 January 2014
Cited by 2 | PDF Full-text (922 KB) | HTML Full-text | XML Full-text
Abstract
A thermophilic fungus previously isolated from composted horse manure was found to produce extracellular iso-RNases that were purified 127.6-fold using a combination of size exclusion chromatography and a novel affinity membrane purification system. The extent of purification was determined electrophoretically using 4%–15% [...] Read more.
A thermophilic fungus previously isolated from composted horse manure was found to produce extracellular iso-RNases that were purified 127.6-fold using a combination of size exclusion chromatography and a novel affinity membrane purification system. The extent of purification was determined electrophoretically using 4%–15% gradient polyacrylamide gels. RNase activity was dependent on the presence of a metal co-factor with significantly more activity with Zn2+ or Mn2+ than Mg2+. The RNases exhibited maximum activity at both pH 3.0 and pH 7.0 with no activity at pH 2.0 or 10.0. The optimal temperature for the iso-RNase was 70 °C. The molecular weight of the iso-RNase was determined to be 69 kDa using a Sephadex G-75 column. Full article
(This article belongs to the Special Issue Thermophilic DNases, RNases and Proteases)
Open AccessArticle Genistein Induces Increase in Fluid pH, Na+ and HCO3 Concentration, SLC26A6 and SLC4A4 (NBCe1)-B Expression in the Uteri of Ovariectomized Rats
Int. J. Mol. Sci. 2014, 15(1), 958-976; doi:10.3390/ijms15010958
Received: 24 November 2013 / Revised: 8 December 2013 / Accepted: 29 December 2013 / Published: 10 January 2014
Cited by 9 | PDF Full-text (1826 KB) | HTML Full-text | XML Full-text
Abstract
Genistein has been reported to stimulate luminal HCO3 secretion. We hypothesized that genistein mediates this effect via SLC26A6 and SLC4A4 (NBCe1) transporters. Our study aimed to: investigate changes in uterine fluid pH, Na+ and HCO3 concentration and [...] Read more.
Genistein has been reported to stimulate luminal HCO3 secretion. We hypothesized that genistein mediates this effect via SLC26A6 and SLC4A4 (NBCe1) transporters. Our study aimed to: investigate changes in uterine fluid pH, Na+ and HCO3 concentration and expression of uterine SLC26A6 and NBCe1 under genistein effect. Ovariectomized adult female rats received 25, 50 and 100 mg/kg/day genistein for a week with and without ICI 182780. A day after the last injection, in vivo uterine perfusion was performed to collect uterine fluid for Na+, HCO3 and pH determination. The animals were then sacrificed and uteri were removed for mRNA and protein expression analyses. SLC26A6 and NBCe1-A and NBCe1-B distribution were visualized by immunohistochemistry (IHC). Genistein at 50 and 100 mg/kg/day stimulates uterine fluid pH, Na+ and HCO3 concentration increase. Genistein at 100 mg/kg/day up-regulates the expression of SLC26A6 and SLC4A4 mRNA, which were reduced following concomitant ICI 182780 administration. In parallel, SLC26A6 and NBCe1-B protein expression were also increased following high dose genistein treatment and were localized mainly at the apical membrane of the luminal epithelia. SLC26A6 and NBCe1-B up-regulation by genistein could be responsible for the observed increase in the uterine fluid pH, Na+ and HCO3 concentration under this condition. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Serum Starvation-Induced Voltage-Gated Potassium Channel Kv7.5 Expression and Its Regulation by Sp1 in Canine Osteosarcoma Cells
Int. J. Mol. Sci. 2014, 15(1), 977-993; doi:10.3390/ijms15010977
Received: 19 October 2013 / Revised: 20 December 2013 / Accepted: 30 December 2013 / Published: 10 January 2014
Cited by 3 | PDF Full-text (534 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The KCNQ gene family, whose members encode Kv7 channels, belongs to the voltage-gated potassium (Kv) channel group. The roles of this gene family have been widely investigated in nerve and muscle cells. In the present study, we investigated several characteristics of Kv7.5, [...] Read more.
The KCNQ gene family, whose members encode Kv7 channels, belongs to the voltage-gated potassium (Kv) channel group. The roles of this gene family have been widely investigated in nerve and muscle cells. In the present study, we investigated several characteristics of Kv7.5, which is strongly expressed in the canine osteosarcoma cell line, CCL-183. Serum starvation upregulated Kv7.5 expression, and the Kv7 channel opener, flupirtine, attenuated cell proliferation by arresting cells in the G0/G1 phase. We also showed that Kv7.5 knockdown helps CCL-183 cells to proliferate. In an effort to find an endogenous regulator of Kv7.5, we used mithramycin A to reduce the level of the transcription factor Sp1, and it strongly inhibited the induction of Kv7.5 in CCL-183 cells. These results suggest that the activation of Kv7.5 by flupirtine may exert an anti-proliferative effect in canine osteosarcoma. Therefore, Kv7.5 is a possible molecular target for canine osteosarcoma therapy. Full article
Open AccessArticle Development of Microsatellite Markers in the Branched Broomrape Phelipanche ramosa L. (Pomel) and Evidence for Host-Associated Genetic Divergence
Int. J. Mol. Sci. 2014, 15(1), 994-1002; doi:10.3390/ijms15010994
Received: 21 November 2013 / Revised: 7 January 2014 / Accepted: 8 January 2014 / Published: 13 January 2014
Cited by 3 | PDF Full-text (192 KB) | HTML Full-text | XML Full-text
Abstract
Phelipanche ramosa is a parasitic plant that infects numerous crops worldwide. In Western Europe it recently expanded to a new host crop, oilseed rape, in which it can cause severe yield losses. We developed 13 microsatellite markers for P. ramosa using next-generation [...] Read more.
Phelipanche ramosa is a parasitic plant that infects numerous crops worldwide. In Western Europe it recently expanded to a new host crop, oilseed rape, in which it can cause severe yield losses. We developed 13 microsatellite markers for P. ramosa using next-generation 454 sequencing data. The polymorphism at each locus was assessed in a sample of 96 individuals collected in France within 6 fields cultivated with tobacco, hemp or oilseed rape. Two loci were monomorphic. At the other 11 loci, the number of alleles and the expected heterozygosity ranged from 3 to 6 and from 0.31 to 0.60, respectively. Genetic diversity within each cultivated field was very low. The host crop from which individuals were collected was the key factor structuring genetic variation. Individuals collected on oilseed rape were strongly differentiated from individuals collected on hemp or tobacco, which suggests that P. ramosa infecting oilseed rape forms a genetically diverged race. The microsatellites we developed will be useful for population genetics studies and for elucidating host-associated genetic divergence in P. ramosa. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Figures

Open AccessArticle Lactoferrin Directly Scavenges Hydroxyl Radicals and Undergoes Oxidative Self-Degradation: A Possible Role in Protection against Oxidative DNA Damage
Int. J. Mol. Sci. 2014, 15(1), 1003-1013; doi:10.3390/ijms15011003
Received: 19 November 2013 / Revised: 24 December 2013 / Accepted: 9 January 2014 / Published: 14 January 2014
Cited by 6 | PDF Full-text (1525 KB) | HTML Full-text | XML Full-text
Abstract
In this study, we examined the protective effect of lactoferrin against DNA damage induced by various hydroxyl radical generation systems. Lactoferrin (LF) was examined with regard to its potential role as a scavenger against radical oxygen species using bovine milk LF. Native [...] Read more.
In this study, we examined the protective effect of lactoferrin against DNA damage induced by various hydroxyl radical generation systems. Lactoferrin (LF) was examined with regard to its potential role as a scavenger against radical oxygen species using bovine milk LF. Native LF, iron-saturated LF (holo-LF), and apolactoferrin (apo-LF) effectively suppressed strand breaks in plasmid DNA due to hydroxyl radicals produced by the Fenton reaction. In addition, both native LF and holo-LF clearly protected calf thymus DNA from fragmentation due to ultraviolet irradiation in the presence of H2O2. We also demonstrated a protective effect of all three LF molecules against 8-hydroxydeoxyguanosine (8-OHdG) formation in calf thymus DNA following ultraviolet (UV) irradiation with H2O2. Our results clearly indicate that native LF has reactive oxygen species-scavenging ability, independent of its nature as a masking component for transient metals. We also demonstrated that the protective effect of LF against oxidative DNA damage is due to degradation of LF itself, which is more susceptible to degradation than other bovine milk proteins. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Structural Characterization of the Degradation Products of a Minor Natural Sweet Diterpene Glycoside Rebaudioside M under Acidic Conditions
Int. J. Mol. Sci. 2014, 15(1), 1014-1025; doi:10.3390/ijms15011014
Received: 21 November 2013 / Revised: 31 December 2013 / Accepted: 9 January 2014 / Published: 14 January 2014
Cited by 1 | PDF Full-text (215 KB) | HTML Full-text | XML Full-text
Abstract
Degradation of rebaudioside M, a minor sweet component of Stevia rebaudiana Bertoni, under conditions that simulated extreme pH and temperature conditions has been studied. Thus, rebaudioside M was treated with 0.1 M phosphoric acid solution (pH 2.0) and 80 °C temperature for [...] Read more.
Degradation of rebaudioside M, a minor sweet component of Stevia rebaudiana Bertoni, under conditions that simulated extreme pH and temperature conditions has been studied. Thus, rebaudioside M was treated with 0.1 M phosphoric acid solution (pH 2.0) and 80 °C temperature for 24 h. Experimental results indicated that rebaudioside M under low pH and higher temperature yielded three minor degradation compounds, whose structural characterization was performed on the basis of 1D (1H-, 13C-) & 2D (COSY, HSQC, HMBC) NMR, HRMS, MS/MS spectral data as well as enzymatic and acid hydrolysis studies. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Evaluation of Hepatic Tissue Blood Flow Using Xenon Computed Tomography with Fibrosis Progression in Nonalcoholic Fatty Liver Disease: Comparison with Chronic Hepatitis C
Int. J. Mol. Sci. 2014, 15(1), 1026-1039; doi:10.3390/ijms15011026
Received: 6 November 2013 / Revised: 24 December 2013 / Accepted: 27 December 2013 / Published: 14 January 2014
Cited by 1 | PDF Full-text (1510 KB) | HTML Full-text | XML Full-text
Abstract
Aims: The present study evaluated the utility of xenon computed tomography (Xe-CT) as a noninvasive diagnostic procedure for the measurement of hepatic tissue blood flow (TBF) in patients with nonalcoholic fatty liver disease (NAFLD) or chronic hepatitis C (CH-C). Methods: Xe-CT was [...] Read more.
Aims: The present study evaluated the utility of xenon computed tomography (Xe-CT) as a noninvasive diagnostic procedure for the measurement of hepatic tissue blood flow (TBF) in patients with nonalcoholic fatty liver disease (NAFLD) or chronic hepatitis C (CH-C). Methods: Xe-CT was performed in 93 patients with NAFLD and in 109 patients with CH-C. Subjects were classified into one of three groups, based on fibrosis stage: group 1, no bridging fibrosis; group 2, bridging fibrosis; and group 3, liver cirrhosis. Correlations between hepatic TBFs in each fibrosis stage were examined. Results: In group 1, portal venous TBF (PVTBF), hepatic arterial (HATBF), and total hepatic TBF (THTBF) were significantly lower in patients with in nonalcoholic steatohepatitis (NASH) than in those with CH-C (p < 0.001, p < 0.05, p < 0.001, respectively). In group 2, PVTBF and THTBF were significantly lower in patients with in NASH than in those with CH-C (p < 0.001, p < 0.05, respectively). In group 3, hepatic TBFs were not significantly different when comparing patients with NASH and those with CH-C. Conclusions: PVTBF decreased due to fat infiltration. Therefore, hemodynamic changes occur relatively earlier in NAFLD than in CH-C. Patients with NASH should be monitored carefully for portal hypertensive complications in the early fibrosis stage. Full article
(This article belongs to the Special Issue Non-Alcoholic Fatty Liver Disease Research)
Open AccessArticle In Vitro Phosphorylation Does not Influence the Aggregation Kinetics of WT α-Synuclein in Contrast to Its Phosphorylation Mutants
Int. J. Mol. Sci. 2014, 15(1), 1040-1067; doi:10.3390/ijms15011040
Received: 17 October 2013 / Revised: 6 January 2014 / Accepted: 7 January 2014 / Published: 15 January 2014
Cited by 7 | PDF Full-text (4216 KB) | HTML Full-text | XML Full-text
Abstract
The aggregation of alpha-synuclein (α-SYN) into fibrils is characteristic for several neurodegenerative diseases, including Parkinson’s disease (PD). Ninety percent of α-SYN deposited in Lewy Bodies, a pathological hallmark of PD, is phosphorylated on serine129. α-SYN can also be phosphorylated on tyrosine125, which [...] Read more.
The aggregation of alpha-synuclein (α-SYN) into fibrils is characteristic for several neurodegenerative diseases, including Parkinson’s disease (PD). Ninety percent of α-SYN deposited in Lewy Bodies, a pathological hallmark of PD, is phosphorylated on serine129. α-SYN can also be phosphorylated on tyrosine125, which is believed to regulate the membrane binding capacity and thus possibly its normal function. A better understanding of the effect of phosphorylation on the aggregation of α-SYN might shed light on its role in the pathogenesis of PD. In this study we compare the aggregation properties of WT α-SYN with the phospho-dead and phospho-mimic mutants S129A, S129D, Y125F and Y125E and in vitro phosphorylated α-SYN using turbidity, thioflavin T and circular dichroism measurements as well as transmission electron microscopy. We show that the mutants S129A and S129D behave similarly compared to wild type (WT) α-SYN, while the mutants Y125F and Y125E fibrillate significantly slower, although all mutants form fibrillar structures similar to the WT protein. In contrast, in vitro phosphorylation of α-SYN on either S129 or Y125 does not significantly affect the fibrillization kinetics. Moreover, FK506 binding proteins (FKBPs), enzymes with peptidyl-prolyl cis-trans isomerase activity, still accelerate the aggregation of phosphorylated α-SYN in vitro, as was shown previously for WT α-SYN. In conclusion, our results illustrate that phosphorylation mutants can display different aggregation properties compared to the more biologically relevant phosphorylated form of α-SYN. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessCommunication Identification of the High Molecular Weight Isoform of Phostensin
Int. J. Mol. Sci. 2014, 15(1), 1068-1079; doi:10.3390/ijms15011068
Received: 11 December 2013 / Revised: 31 December 2013 / Accepted: 6 January 2014 / Published: 15 January 2014
PDF Full-text (2314 KB) | HTML Full-text | XML Full-text
Abstract
Phostensin is encoded by KIAA1949. 5'-RACEanalysis has been used to identify the translation start site of phostensin mRNA, indicating that it encodes 165 amino acids with an apparent molecular weight of 26 kDa on SDS-PAGE. This low-molecular-weight phostensin is present in [...] Read more.
Phostensin is encoded by KIAA1949. 5'-RACEanalysis has been used to identify the translation start site of phostensin mRNA, indicating that it encodes 165 amino acids with an apparent molecular weight of 26 kDa on SDS-PAGE. This low-molecular-weight phostensin is present in human peripheral blood mononuclear cells and many leukemic cell lines. Phostensin is a protein phosphatase-1(PP1) binding protein. It also contains one actin-binding motif at its C-terminal region and binds to the pointed ends of actin filaments, modulating actin dynamics. In the current study, a high-molecular-weight phostensin is identified by using immunoprecipitationin combination with a proteomic approach. This new species of phostensin is also encoded by KIAA1949 and consists of 613 amino acids with an apparent molecular weight of 110 kDa on SDS-PAGE. The low-molecular-weight and high-molecular-weight phostensins were named as phostensin-α and phostensin-β, respectively. Although phostensin-α is the C-terminal region of phostensin-β, it is not degraded from phostensin-β. Phostensin-β is capable of associating with PP1 and actin filaments, and is present in many cell lines. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Mesoscale Characterization of Supramolecular Transient Networks Using SAXS and Rheology
Int. J. Mol. Sci. 2014, 15(1), 1096-1111; doi:10.3390/ijms15011096
Received: 3 November 2013 / Revised: 2 January 2014 / Accepted: 8 January 2014 / Published: 16 January 2014
Cited by 8 | PDF Full-text (1880 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Hydrogels and, in particular, supramolecular hydrogels show promising properties for application in regenerative medicine because of their ability to adapt to the natural environment these materials are brought into. However, only few studies focus on the structure-property relationships in supramolecular hydrogels. Here, [...] Read more.
Hydrogels and, in particular, supramolecular hydrogels show promising properties for application in regenerative medicine because of their ability to adapt to the natural environment these materials are brought into. However, only few studies focus on the structure-property relationships in supramolecular hydrogels. Here, we study in detail both the structure and the mechanical properties of such a network, composed of poly(ethylene glycol), end-functionalized with ureido-pyrimidinone fourfold hydrogen bonding units. This network is responsive to triggers such as concentration, temperature and pH. To obtain more insight into the sol-gel transition of the system, both rheology and small-angle X-ray scattering (SAXS) are used. We show that the sol-gel transitions based on these three triggers, as measured by rheology, coincide with the appearance of a structural feature in SAXS. We attribute this feature to the presence of hydrophobic domains where cross-links are formed. These results provide more insight into the mechanism of network formation in these materials, which can be exploited for tailoring their behavior for biomedical applications, where one of the triggers discussed might be used. Full article
(This article belongs to the Special Issue Synthesis, Characterization and Application of Supramolecular Systems)
Figures

Open AccessArticle Artesunate Reduces Serum Lipopolysaccharide in Cecal Ligation/Puncture Mice via Enhanced LPS Internalization by Macrophages through Increased mRNA Expression of Scavenger Receptors
Int. J. Mol. Sci. 2014, 15(1), 1143-1161; doi:10.3390/ijms15011143
Received: 22 October 2013 / Revised: 2 January 2014 / Accepted: 9 January 2014 / Published: 16 January 2014
Cited by 5 | PDF Full-text (532 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Innate immunity is the first line of defense in human beings against pathogen infection; monocytes/macrophages are the primary cells of the innate immune system. Recently, macrophages/monocytes have been discovered to participate in LPS clearance, and the clearance efficiency determines the magnitude of [...] Read more.
Innate immunity is the first line of defense in human beings against pathogen infection; monocytes/macrophages are the primary cells of the innate immune system. Recently, macrophages/monocytes have been discovered to participate in LPS clearance, and the clearance efficiency determines the magnitude of the inflammatory response and subsequent organ injury. Previously, we reported that artesunate (AS) protected sepsis mice against heat-killed E. coli challenge. Herein, we further confirmed that AS protected cecal ligation/puncture (CLP) sepsis mice. Its protection on sepsis mice was related to not only reduction of pro-inflammatory cytokines and serum LPS levels but also improvement of liver function. Based on the fact that AS did not directly bind and neutralize LPS, we hypothesized that the reduction of serum LPS level might be related to enhancement of LPS internalization and subsequent detoxification. Our results showed that AS increased FITC-LPS internalization by peritoneal macrophage and liver Kupffer cell, but enhancement of LPS internalization by AS was not related to the clathrin-dependent pathway. However, AS induced mRNA expression of important scavenger receptors (SRs); SR-A and MARCO mRNA expression was upregulated, suggesting that AS enhancement of LPS internalization and inhibition of pro-inflammatory cytokines was related to changes in mRNA expression of SRs. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Optimization and Evaluation of Magnetic Bead Separation Combined with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectroscopy (MALDI-TOF MS) for Proteins Profiling of Peritoneal Dialysis Effluent
Int. J. Mol. Sci. 2014, 15(1), 1162-1175; doi:10.3390/ijms15011162
Received: 29 October 2013 / Revised: 4 January 2014 / Accepted: 10 January 2014 / Published: 16 January 2014
Cited by 2 | PDF Full-text (741 KB) | HTML Full-text | XML Full-text
Abstract
Peritoneal dialysis effluent (PDE) potentially carries an archive of peptides relevant to pathological processes in abdominal and surrounding tissues. Magnetic beads and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is one such approach that offers a unique tool for profiling of peptides, but [...] Read more.
Peritoneal dialysis effluent (PDE) potentially carries an archive of peptides relevant to pathological processes in abdominal and surrounding tissues. Magnetic beads and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is one such approach that offers a unique tool for profiling of peptides, but this approach has not been used in the PDE analysis. In this study, we developed a strategy for screening PDE proteins <15 kDa and applied this technique to identify potential biomarkers for peritonitis. We examined four kinds of magnetic beads, including a carbon series (C3, C8), weak cation exchange (WCX) and immobilized metal-affinity chromatography (IMAC-Cu) beads. Samples processed with IMAC-Cu magnetic beads consistently showed more MS signals across all beads within the measured mass range. Moreover, there was no difference in the number and morphology of MS signals between concentrated and unconcentrated samples. The PDE peptidome pattern, based on a panel of 15 peaks, accurately recognized peritonitis PD patients from peritonitis-free patients with sensitivity of 90.5% and specificity of 94.7% respectively. Therefore, IMAC-Cu magnetic beads and unconcentrated samples can be used as a fast and cost-effective approach for sample preparation prior to more in-depth discovery of predictive biomarkers of disease in patients on dialysis. Full article
(This article belongs to the collection Advances in Proteomic Research)
Open AccessArticle Leptin Activates RhoA/ROCK Pathway to Induce Cytoskeleton Remodeling in Nucleus Pulposus Cells
Int. J. Mol. Sci. 2014, 15(1), 1176-1188; doi:10.3390/ijms15011176
Received: 30 November 2013 / Revised: 3 January 2014 / Accepted: 8 January 2014 / Published: 16 January 2014
Cited by 1 | PDF Full-text (1022 KB) | HTML Full-text | XML Full-text
Abstract
Hyperleptinemia is implicated in obesity-associated lumbar disc degeneration. Nevertheless, the effect of leptin on the intracellular signaling of nucleus pulposus cells is not clear. The current study sought to delineate the possible involvement of the RhoA/ROCK pathway in leptin-mediated cytoskeleton reorganization in [...] Read more.
Hyperleptinemia is implicated in obesity-associated lumbar disc degeneration. Nevertheless, the effect of leptin on the intracellular signaling of nucleus pulposus cells is not clear. The current study sought to delineate the possible involvement of the RhoA/ROCK pathway in leptin-mediated cytoskeleton reorganization in nucleus pulposus cells. Nucleus pulposus cells isolated from scoliosis patients were treated with 10 ng/mL of leptin. Fluorescent resonance energy transfer analysis was used to determine the activation of RhoA signaling in nucleus pulposus cells. The protein expression of LIMK1 and cofilin-2 were analyzed by western blot analysis. F-actin cytoskeletal reorganization was assessed by rhodamine-conjugated phalloidin immunoprecipitation. Leptin induced F-actin reorganization and stress fiber formation in nucleus pulposus cells, accompanied by localized RhoA activation and phosphorylation of LIMK1 and cofilin. The RhoA inhibitor C3 exoenzyme or the ROCK inhibitor Y-27632 potently attenuated the effects of leptin on F-actin reorganization and stress fiber formation. Both inhibitors also prevented leptin-induced phosphorylation of LIMK1 and cofilin-2. Our study demonstrated that leptin activated the RhoA/ROCK/LIMK/cofilin-2 cascade to induce cytoskeleton reorganization in nucleus pulposus cells. These findings may provide novel insights into the pathogenic mechanism of obesity-associated lumbar disc degeneration. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessCommunication Clinical Evaluation of Extracellular ADMA Concentrations in Human Blood and Adipose Tissue
Int. J. Mol. Sci. 2014, 15(1), 1189-1200; doi:10.3390/ijms15011189
Received: 10 December 2013 / Revised: 7 January 2014 / Accepted: 8 January 2014 / Published: 17 January 2014
Cited by 3 | PDF Full-text (246 KB) | HTML Full-text | XML Full-text
Abstract
Circulating asymmetrical dimethylarginine (ADMA), an endogenous inhibitor of nitric oxide synthesis, has been proposed as a biomarker for clinical outcome. Dimethylarginine dimethylaminohydrolase (DDAH) is the main enzyme responsible for ADMA metabolism and elimination. Adipose tissue ADMA concentrations and DDAH activity and their [...] Read more.
Circulating asymmetrical dimethylarginine (ADMA), an endogenous inhibitor of nitric oxide synthesis, has been proposed as a biomarker for clinical outcome. Dimethylarginine dimethylaminohydrolase (DDAH) is the main enzyme responsible for ADMA metabolism and elimination. Adipose tissue ADMA concentrations and DDAH activity and their role in diabetes and obesity have not yet been investigated. In this study, we evaluated clinical microdialysis in combination with a sensitive analytical method (GC-MS/MS) to measure ADMA concentrations in extracellular fluid. Adipose tissue ADMA concentrations were assessed before and during an oral glucose tolerance test in lean healthy subjects and subjects with diabetes (n = 4 each), and in morbidly obese subjects before and after weight loss of 30 kg (n = 7). DDAH activity was determined in subcutaneous and visceral adipose tissue obtained during laparoscopic surgery (n = 5 paired samples). Mean interstitial ADMA concentrations did not differ between study populations (healthy 0.17 ± 0.03 µM; diabetic 0.21 ± 0.03 µM; morbidly obese 0.16 ± 0.01 and 0.17 ± 0.01 µM before and after weight loss, respectively). We did not observe any response of interstitial ADMA concentrations to the oral glucose challenge. Adipose tissue DDAH activity was negligible compared to liver tissue. Thus, adipose tissue ADMA plays a minor role in NO-dependent regulation of adipose tissue blood flow and metabolism. Full article
(This article belongs to the Special Issue ADMA and Nitrergic System)
Open AccessArticle Hispolon Decreases Melanin Production and Induces Apoptosis in Melanoma Cells through the Downregulation of Tyrosinase and Microphthalmia-Associated Transcription Factor (MITF) Expressions and the Activation of Caspase-3, -8 and -9
Int. J. Mol. Sci. 2014, 15(1), 1201-1215; doi:10.3390/ijms15011201
Received: 27 November 2013 / Revised: 29 December 2013 / Accepted: 8 January 2014 / Published: 17 January 2014
Cited by 9 | PDF Full-text (1012 KB) | HTML Full-text | XML Full-text
Abstract
Hispolon is one of the most important functional compounds that forms Phellinus linteus (Berkeley & Curtis) Teng. Hispolon has antioxidant, anti-inflammatory, antiproliferative and anticancer effects. In this study, we analyzed the functions of hispolon on melanogenesis and apoptosis in B16-F10 melanoma cells. [...] Read more.
Hispolon is one of the most important functional compounds that forms Phellinus linteus (Berkeley & Curtis) Teng. Hispolon has antioxidant, anti-inflammatory, antiproliferative and anticancer effects. In this study, we analyzed the functions of hispolon on melanogenesis and apoptosis in B16-F10 melanoma cells. The results demonstrated that hispolon is not an enzymatic inhibitor for tyrosinase; rather, it represses the expression of tyrosinase and the microphthalmia-associated transcription factor (MITF) to reduce the production of melanin in α-melanocyte-stimulating hormone (α-MSH)-stimulated B16-F10 cells at lower concentrations (less than 2 μM). In contrast, at higher concentration (greater than 10 μM), hispolon can induce activity of caspase-3, -8 and -9 to trigger apoptosis of B16-F10 cells but not of Detroit 551 normal fibroblast cells. Therefore, we suggest that hispolon has the potential to treat hyperpigmentation diseases and melanoma skin cancer in the future. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Synthesis and Antimicrobial Evaluation of Some Novel Thiazole, Pyridone, Pyrazole, Chromene, Hydrazone Derivatives Bearing a Biologically Active Sulfonamide Moiety
Int. J. Mol. Sci. 2014, 15(1), 1237-1254; doi:10.3390/ijms15011237
Received: 10 November 2013 / Revised: 10 January 2014 / Accepted: 13 January 2014 / Published: 17 January 2014
Cited by 14 | PDF Full-text (300 KB) | HTML Full-text | XML Full-text
Abstract
This study aimed for the synthesis of new heterocyclic compounds incorporating sulfamoyl moiety suitable for use as antimicrobial agents via a versatile, readily accessible N-[4-(aminosulfonyl)phenyl]-2-cyanoacetamide (3). The 2-pyridone derivatives were obtained via reaction of cyanoacetamide with acetylacetone or arylidenes [...] Read more.
This study aimed for the synthesis of new heterocyclic compounds incorporating sulfamoyl moiety suitable for use as antimicrobial agents via a versatile, readily accessible N-[4-(aminosulfonyl)phenyl]-2-cyanoacetamide (3). The 2-pyridone derivatives were obtained via reaction of cyanoacetamide with acetylacetone or arylidenes malononitrile. Cycloaddition reaction of cyanoacetamide with salicyaldehyde furnished chromene derivatives. Diazotization of 3 with the desired diazonium chloride gave the hydrazone derivatives 13ae. Also, the reactivity of the hydrazone towards hydrazine hydrate to give Pyrazole derivatives was studied. In addition, treatment of 3 with elemental sulfur and phenyl isothiocyanate or malononitrile furnished thiazole and thiophene derivatives respectively. Reaction of 3 with phenyl isothiocyanate and KOH in DMF afforded the intermediate salt 17 which reacted in situ with 3-(2-bromoacetyl)-2H-chromen-2-one and methyl iodide afforded the thiazole and ketene N,S-acetal derivatives respectively. Finally, reaction of 3 with carbon disulfide and 1,3-dibromopropane afforded the N-[4-(aminosulfonyl) phenyl]-2-cyano-2-(1,3-dithian-2-ylidene)acetamide product 22. All newly synthesized compounds were elucidated by considering the data of both elemental and spectral analysis. The compounds were evaluated for both their in vitro antibacterial and antifungal activities and showed promising results. Full article
Open AccessArticle The Bioconcentration and Degradation of Nonylphenol and Nonylphenol Polyethoxylates by Chlorella vulgaris
Int. J. Mol. Sci. 2014, 15(1), 1255-1270; doi:10.3390/ijms15011255
Received: 12 December 2013 / Revised: 8 January 2014 / Accepted: 9 January 2014 / Published: 17 January 2014
PDF Full-text (438 KB) | HTML Full-text | XML Full-text
Abstract
Nonylphenol polyethoxylates (NPnEOs), a major class of nonionic surfactants, can easily enter into aquatic environments through various pathways due to their wide applications, which leads to the extensive existence of their relative stable metabolites, namely nonylphenol (NP) and mono- to tri-ethoxylates. This [...] Read more.
Nonylphenol polyethoxylates (NPnEOs), a major class of nonionic surfactants, can easily enter into aquatic environments through various pathways due to their wide applications, which leads to the extensive existence of their relative stable metabolites, namely nonylphenol (NP) and mono- to tri-ethoxylates. This study investigated the bioconcentration and degradation of NP and NPnEO oligomers (n = 1–12) by a green algae, Chlorella vulgaris. Experimental results showed that C. vulgaris can remove NP from water phase efficiently, and bioconcentration and degradation accounted for approximately half of its loss, respectively, with a 48 h BCF (bioconcentration factor) of 2.42 × 103. Moreover, C. vulgaris could concentrate and degrade NPnEOs, distribution profiles of the series homologues of the NPnEOs in algae and water phase were quite different from the initial homologue profile. The 48 h BCF of the NPnEO homologues increased with the length of the EO chain. Degradation extent of total NPnEOs by C. vulgaris was 95.7%, and only 1.1% remained in water phase, and the other 3.2% remained in the algal cells. The algae removed the NPnEOs mainly through degradation. Due to rapid degradation, concentrations of the long chain NPnEO homologous in both water (n ≥ 2) and the algal phase (n ≥ 5) was quite low at the end of a 48 h experiment. Full article
Open AccessArticle Re-Evaluation of Binding Properties of Recombinant Lymphocyte Receptors NKR-P1A and CD69 to Chemically Synthesized Glycans and Peptides
Int. J. Mol. Sci. 2014, 15(1), 1271-1283; doi:10.3390/ijms15011271
Received: 6 November 2013 / Revised: 19 December 2013 / Accepted: 3 January 2014 / Published: 17 January 2014
Cited by 5 | PDF Full-text (1335 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The binding of monosaccharides and short peptides to lymphocyte receptors (human CD69 and rat NKR-P1A) was first reported in 1994 and then in a number of subsequent publications. Based on this observation, numerous potentially high-affinity saccharide ligands have been synthesized over the [...] Read more.
The binding of monosaccharides and short peptides to lymphocyte receptors (human CD69 and rat NKR-P1A) was first reported in 1994 and then in a number of subsequent publications. Based on this observation, numerous potentially high-affinity saccharide ligands have been synthesized over the last two decades in order to utilize their potential in antitumor therapy. Due to significant inconsistencies in their reported binding properties, we decided to re-examine the interaction between multiple ligands and CD69 or NKR-P1A. Using NMR titration and isothermal titration calorimetry we were unable to detect the binding of the tested ligands such as N-acetyl-d-hexosamines and oligopeptides to both receptors, which contradicts the previous observations published in more than twenty papers over the last fifteen years. Full article
(This article belongs to the Section Molecular Recognition)
Open AccessArticle Rapid and Efficient Functionalized Ionic Liquid-Catalyzed Aldol Condensation Reactions Associated with Microwave Irradiation
Int. J. Mol. Sci. 2014, 15(1), 1284-1299; doi:10.3390/ijms15011284
Received: 28 November 2013 / Revised: 17 December 2013 / Accepted: 17 December 2013 / Published: 17 January 2014
Cited by 7 | PDF Full-text (315 KB) | HTML Full-text | XML Full-text
Abstract
Five quaternary ammonium ionic liquid (IL) and two tetrabutylphosphonium ILs were prepared and characterized. An environmentally benign and convenient functionalized ionic liquid catalytic system was thus explored in the aldol condensation reactions of aromatic aldehydes with acetone. The aldol reactions proceeded more [...] Read more.
Five quaternary ammonium ionic liquid (IL) and two tetrabutylphosphonium ILs were prepared and characterized. An environmentally benign and convenient functionalized ionic liquid catalytic system was thus explored in the aldol condensation reactions of aromatic aldehydes with acetone. The aldol reactions proceeded more efficiently through microwave-assisted heating than through conventional thermal heating. The yield of products obtained under microwave heating for 30 min was approximately 90%, and the ILs can be recovered and reused at least five times without apparent loss of activity. In addition, this catalytic system can be successfully extended to the Henry reactions. Full article
(This article belongs to the Special Issue Ionic Liquids 2014 & Selected Papers from ILMAT 2013)
Open AccessArticle Purification of an Inducible DNase from a Thermophilic Fungus
Int. J. Mol. Sci. 2014, 15(1), 1300-1314; doi:10.3390/ijms15011300
Received: 6 December 2013 / Revised: 6 January 2014 / Accepted: 9 January 2014 / Published: 20 January 2014
Cited by 1 | PDF Full-text (832 KB) | HTML Full-text | XML Full-text
Abstract
The ability to induce an extracellular DNase from a novel thermophilic fungus was studied and the DNAse purified using both traditional and innovative purification techniques. The isolate produced sterile hyphae under all attempted growing conditions, with an average diameter of 2 µm [...] Read more.
The ability to induce an extracellular DNase from a novel thermophilic fungus was studied and the DNAse purified using both traditional and innovative purification techniques. The isolate produced sterile hyphae under all attempted growing conditions, with an average diameter of 2 µm and was found to have an optimal temperature of 45 °C and a maximum of 65 °C. Sequencing of the internal transcribed region resulted in a 91% match with Chaetomium sp., suggesting a new species, but further clarification on this point is needed. The optimal temperature for DNase production was found to be 55 °C and was induced by the presence of DNA and/or deoxyribose. Static growth of the organism resulted in significantly higher DNase production than agitated growth. The DNase was purified 145-fold using a novel affinity membrane purification system with 25% of the initial enzyme activity remaining. Electrophoresis of the purified enzyme resulted in a single protein band, indicating DNase homogeneity. Full article
(This article belongs to the Special Issue Thermophilic DNases, RNases and Proteases)
Open AccessArticle Development of Molecularly Imprinted Polymer in Porous Film Format for Binding of Phenol and Alkylphenols from Water
Int. J. Mol. Sci. 2014, 15(1), 1338-1357; doi:10.3390/ijms15011338
Received: 16 November 2013 / Revised: 4 January 2014 / Accepted: 9 January 2014 / Published: 20 January 2014
Cited by 2 | PDF Full-text (1291 KB) | HTML Full-text | XML Full-text
Abstract
Molecularly imprinted polymers (MIPs) were fabricated on glass slides with a “sandwich” technique giving ~20 µm thick films. Methanol/water as a solvent, and polyethyleneglycol and polyvinylacetate as solvent modifiers, were used to give a porous morphology, which was studied with scanning electron [...] Read more.
Molecularly imprinted polymers (MIPs) were fabricated on glass slides with a “sandwich” technique giving ~20 µm thick films. Methanol/water as a solvent, and polyethyleneglycol and polyvinylacetate as solvent modifiers, were used to give a porous morphology, which was studied with scanning electron microscopy and gravimetric analysis. Various MIPs were synthesized through non-covalent imprinting with phenol as the template; itaconic acid, 4-vinylpyridine, and styrene as monomers; ethylene glycol dimethacrylate, triethylene glycol dimethacrylate, and pentaerythritol triacrylate (PETA) as cross-linkers. Binding and imprinting properties of the MIPs were evaluated based on phenol adsorption isotherms. Since phenol has only one weakly acidic hydroxyl group and lacks unique structural characteristics necessary for binding specificity, the preparation of selective MIPs was challenging. The recognition of phenol via hydrogen bonding is suppressed in water, while hydrophobic interactions, though promoted, are not specific enough for highly-selective phenol recognition. Nevertheless, the styrene-PETA MIP gave modest imprinting effects, which were higher at lower concentrations (Imprinting Factor (IF) = 1.16 at 0.5 mg·L−1). The isotherm was of a Freundlich type over 0.1–40 mg·L−1 and there was broad cross-reactivity towards other structurally similar phenols. This shows that phenol MIPs or simple adsorbents can be developed based on styrene for hydrophobic binding, and PETA to form a tighter, hydrophilic network. Full article
(This article belongs to the Section Molecular Recognition)
Figures

Open AccessArticle Extracellular Disposal of Tumor-Suppressor miRs-145 and -34a via Microvesicles and 5-FU Resistance of Human Colon Cancer Cells
Int. J. Mol. Sci. 2014, 15(1), 1392-1401; doi:10.3390/ijms15011392
Received: 8 November 2013 / Revised: 7 January 2014 / Accepted: 8 January 2014 / Published: 20 January 2014
Cited by 7 | PDF Full-text (531 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The dysregulation of microRNA (miRNA) expression causes various kinds of diseases. Especially, alterations in miRNA expression levels are frequently observed in human tumor cells and are associated with cancer pathogenesis. Earlier we established Fluorouracil (5-FU)-resistant human colon cancer DLD-1 cells (DLD-1/5FU) from [...] Read more.
The dysregulation of microRNA (miRNA) expression causes various kinds of diseases. Especially, alterations in miRNA expression levels are frequently observed in human tumor cells and are associated with cancer pathogenesis. Earlier we established Fluorouracil (5-FU)-resistant human colon cancer DLD-1 cells (DLD-1/5FU) from parental 5-FU- sensitive DLD-1 cells. In the present study, we examined the expression of miRNA in each cell line and in its extracellular microvesicles (MVs) before and after treatment with 5-FU. The nascent RNAs of anti-oncogenic miR-34a and -145 labeled with EU in both cells were proved to be transferred into MVs in both cell lines. The levels of miR-34a and -145 in the cells and in their MVs were not largely different in the two cell lines, and a substantial amount of both miRNAs was secreted by both cell lines even in the steady-state condition. The exposure of both cell lines to 5-FU significantly increased the intracellular levels of miR-145 and miR-34a in the 5-FU-sensitive DLD-1 cells, whereas the level of neither miR was elevated in the DLD-1/5FU cells. Interestingly, the amount of miR-145 detected in the small MVs shed into the medium of the parental cells was reduced after the treatment with 5-FU. On the other hand, the intracellular expression of miR-34a in the DLD-1/5FU cells was down-regulated compared with that in the parental DLD-1 cells even in the steady-state condition. As to the miR-34a secreted into MVs, the increase in the level in DLD-1/5FU cells was greater than that in the parental DLD-1 cells after the treatment with 5-FU. Thus, the intra- and extracellular miR-145 and -34a were closely associated with 5-FU resistance, and the resistance was in part due to the enhanced secretion of miR-145 and -34a via MVs, resulting in low intracellular levels of both miRNAs. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Phenoxybenzamine Is Neuroprotective in a Rat Model of Severe Traumatic Brain Injury
Int. J. Mol. Sci. 2014, 15(1), 1402-1417; doi:10.3390/ijms15011402
Received: 25 November 2013 / Revised: 1 January 2014 / Accepted: 14 January 2014 / Published: 20 January 2014
Cited by 1 | PDF Full-text (471 KB) | HTML Full-text | XML Full-text
Abstract
Phenoxybenzamine (PBZ) is an FDA approved α-1 adrenergic receptor antagonist that is currently used to treat symptoms of pheochromocytoma. However, it has not been studied as a neuroprotective agent for traumatic brain injury (TBI). While screening neuroprotective candidates, we found that phenoxybenzamine [...] Read more.
Phenoxybenzamine (PBZ) is an FDA approved α-1 adrenergic receptor antagonist that is currently used to treat symptoms of pheochromocytoma. However, it has not been studied as a neuroprotective agent for traumatic brain injury (TBI). While screening neuroprotective candidates, we found that phenoxybenzamine reduced neuronal death in rat hippocampal slice cultures following exposure to oxygen glucose deprivation (OGD). Using this system, we found that phenoxybenzamine reduced neuronal death over a broad dose range (0.1 µM–1 mM) and provided efficacy when delivered up to 16 h post-OGD. We further tested phenoxybenzamine in the rat lateral fluid percussion model of TBI. When administered 8 h after TBI, phenoxybenzamine improved neurological severity scoring and foot fault assessments. At 25 days post injury, phenoxybenzamine treated TBI animals also showed a significant improvement in both learning and memory compared to saline treated controls. We further examined gene expression changes within the cortex following TBI. At 32 h post-TBI phenoxybenzamine treated animals had significantly lower expression of pro-inflammatory signaling proteins CCL2, IL1β, and MyD88, suggesting that phenoxybenzamine may exert a neuroprotective effect by reducing neuroinflammation after TBI. These data suggest that phenonxybenzamine may have application in the treatment of TBI. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2014)
Open AccessArticle Circulating MicroRNAs as Biomarkers of Acute Stroke
Int. J. Mol. Sci. 2014, 15(1), 1418-1432; doi:10.3390/ijms15011418
Received: 13 November 2013 / Revised: 20 December 2013 / Accepted: 7 January 2014 / Published: 20 January 2014
Cited by 21 | PDF Full-text (1504 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
MicroRNAs have been identified as key regulators of gene expression and thus their potential in disease diagnostics, prognosis and therapy is being actively pursued. Deregulation of microRNAs in cerebral pathogenesis has been reported to a limited extent in both animal models and [...] Read more.
MicroRNAs have been identified as key regulators of gene expression and thus their potential in disease diagnostics, prognosis and therapy is being actively pursued. Deregulation of microRNAs in cerebral pathogenesis has been reported to a limited extent in both animal models and human. Due to the complexity of the pathology, identifying stroke specific microRNAs has been a challenge. This study shows that microRNA profiles reflect not only the temporal progression of stroke but also the specific etiologies. A panel of 32 microRNAs, which could differentiate stroke etiologies during acute phase was identified and verified using a customized TaqMan Low Density Array (TLDA). Furthermore we also found 5 microRNAs, miR-125b-2*, -27a*, -422a, -488 and -627 to be consistently altered in acute stroke irrespective of age or severity or confounding metabolic complications. Differential expression of these 5 microRNAs was also observed in rat stroke models. Hence, their specificity to the stroke pathology emphasizes the possibility of developing these microRNAs into accurate and useful tools for diagnosis of stroke. Full article
(This article belongs to the Special Issue Neurological Injuries’ Monitoring, Tracking and Treatment)
Open AccessCommunication Low Prostate Concentration of Lycopene Is Associated with Development of Prostate Cancer in Patients with High-Grade Prostatic Intraepithelial Neoplasia
Int. J. Mol. Sci. 2014, 15(1), 1433-1440; doi:10.3390/ijms15011433
Received: 10 October 2013 / Revised: 11 December 2013 / Accepted: 8 January 2014 / Published: 21 January 2014
Cited by 8 | PDF Full-text (268 KB) | HTML Full-text | XML Full-text
Abstract
Prostate cancer (PC) is a frequent male malignancy and represents the second most diagnosed cancer in men. Since pre-cancerous lesions, i.e., the high-grade prostatic intraepithelial neoplasia (HGPIN), can be detected years before progression to PC, early diagnosis and chemoprevention are targeted [...] Read more.
Prostate cancer (PC) is a frequent male malignancy and represents the second most diagnosed cancer in men. Since pre-cancerous lesions, i.e., the high-grade prostatic intraepithelial neoplasia (HGPIN), can be detected years before progression to PC, early diagnosis and chemoprevention are targeted strategies to reduce PC rates. Animal studies have shown that lycopene, a carotenoid contained in tomatoes, is a promising candidate for the chemoprevention of PC. However, its efficacy in humans remains controversial. The present study aimed to investigate the relevance of plasma and prostate concentration of lycopene after a lycopene-enriched diet in patients diagnosed with HGPIN. Thirty-two patients diagnosed with HGPIN were administered a lycopene-enriched diet (20–25 mg/day of lycopene; through 30 g/day of triple concentrated tomato paste) for 6 months. A 6-month follow-up prostate biopsy assessed progression to PC. Patients were classified into three groups according to the histopathological features of the 6-month follow-up biopsy results: prostatitis; HGPIN and PC. PSA and plasma lycopene levels were measured before and after the dietary lycopene supplementation. Prostatic lycopene concentration was only assessed after the supplementation diet. Only prostatic lycopene concentration showed significant differences between the three groups (p = 0.03). Prostatic lycopene concentration below a 1 ng/mg threshold was associated with PC at 6-month follow-up biopsy (p = 0.003). We observed no overall benefits from a 6-month lycopene supplementation, as the rate of HGPIN progression to PC in our population (9/32, 28%) was similar to rates reported in the literature. Baseline PSA levels also showed no significant changes after a lycopene-enriched diet. Our findings point to prostatic lycopene concentration as a promising biomarker of PC. Further prospective longitudinal studies are needed to assess the prognostic role of prostatic lycopene in PC. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Figures

Open AccessArticle Plant Dependence on Rhizobia for Nitrogen Influences Induced Plant Defenses and Herbivore Performance
Int. J. Mol. Sci. 2014, 15(1), 1466-1480; doi:10.3390/ijms15011466
Received: 19 November 2013 / Revised: 15 January 2014 / Accepted: 15 January 2014 / Published: 21 January 2014
Cited by 5 | PDF Full-text (360 KB) | HTML Full-text | XML Full-text
Abstract
Symbiotic rhizobia induce many changes in legumes that could affect aboveground interactions with herbivores. We explored how changing the intensity of Bradyrhizobium japonicum, as modulated by soil nitrogen (N) levels, influenced the interaction between soybean (Glycine max) and herbivores [...] Read more.
Symbiotic rhizobia induce many changes in legumes that could affect aboveground interactions with herbivores. We explored how changing the intensity of Bradyrhizobium japonicum, as modulated by soil nitrogen (N) levels, influenced the interaction between soybean (Glycine max) and herbivores of different feeding guilds. When we employed a range of fertilizer applications to manipulate soil N, plants primarily dependent on rhizobia for N exhibited increased root nodulation and higher levels of foliar ureides than plants given N fertilizer; yet all treatments maintained similar total N levels. Soybean podworm (Helicoverpa zea) larvae grew best on plants with the highest levels of rhizobia but, somewhat surprisingly, preferred to feed on high-N-fertilized plants when given a choice. Induction of the defense signaling compound jasmonic acid (JA) by H. zea feeding damage was highest in plants primarily dependent on rhizobia. Differences in rhizobial dependency on soybean did not appear to affect interactions with the phloem-feeding soybean aphid (Aphis glycines). Overall, our results suggest that rhizobia association can affect plant nutritional quality and the induction of defense signaling pathways and that these effects may influence herbivore feeding preferences and performance—though such effects may vary considerably for different classes of herbivores. Full article
Figures

Open AccessArticle Dopamine D4 Receptor Counteracts Morphine-Induced Changes in µ Opioid Receptor Signaling in the Striosomes of the Rat Caudate Putamen
Int. J. Mol. Sci. 2014, 15(1), 1481-1498; doi:10.3390/ijms15011481
Received: 30 November 2013 / Revised: 8 January 2014 / Accepted: 13 January 2014 / Published: 21 January 2014
Cited by 2 | PDF Full-text (1442 KB) | HTML Full-text | XML Full-text
Abstract
The mu opioid receptor (MOR) is critical in mediating morphine analgesia. However, prolonged exposure to morphine induces adaptive changes in this receptor leading to the development of tolerance and addiction. In the present work we have studied whether the continuous administration of [...] Read more.
The mu opioid receptor (MOR) is critical in mediating morphine analgesia. However, prolonged exposure to morphine induces adaptive changes in this receptor leading to the development of tolerance and addiction. In the present work we have studied whether the continuous administration of morphine induces changes in MOR protein levels, its pharmacological profile, and MOR-mediated G-protein activation in the striosomal compartment of the rat CPu, by using immunohistochemistry and receptor and DAMGO-stimulated [35S]GTPγS autoradiography. MOR immunoreactivity, agonist binding density and its coupling to G proteins are up-regulated in the striosomes by continuous morphine treatment in the absence of changes in enkephalin and dynorphin mRNA levels. In addition, co-treatment of morphine with the dopamine D4 receptor (D4R) agonist PD168,077 fully counteracts these adaptive changes in MOR, in spite of the fact that continuous PD168,077 treatment increases the [3H]DAMGO Bmax values to the same degree as seen after continuous morphine treatment. Thus, in spite of the fact that both receptors can be coupled to Gi/0 protein, the present results give support for the existence of antagonistic functional D4R-MOR receptor-receptor interactions in the adaptive changes occurring in MOR of striosomes on continuous administration of morphine. Full article
(This article belongs to the collection G Protein-Coupled Receptor Signaling and Regulation)
Open AccessArticle Genetic Deletion of Rheb1 in the Brain Reduces Food Intake and Causes Hypoglycemia with Altered Peripheral Metabolism
Int. J. Mol. Sci. 2014, 15(1), 1499-1510; doi:10.3390/ijms15011499
Received: 16 November 2013 / Revised: 12 December 2013 / Accepted: 7 January 2014 / Published: 21 January 2014
Cited by 2 | PDF Full-text (1071 KB) | HTML Full-text | XML Full-text
Abstract
Excessive food/energy intake is linked to obesity and metabolic disorders, such as diabetes. The hypothalamus in the brain plays a critical role in the control of food intake and peripheral metabolism. The signaling pathways in hypothalamic neurons that regulate food intake and [...] Read more.
Excessive food/energy intake is linked to obesity and metabolic disorders, such as diabetes. The hypothalamus in the brain plays a critical role in the control of food intake and peripheral metabolism. The signaling pathways in hypothalamic neurons that regulate food intake and peripheral metabolism need to be better understood for developing pharmacological interventions to manage eating behavior and obesity. Mammalian target of rapamycin (mTOR), a serine/threonine kinase, is a master regulator of cellular metabolism in different cell types. Pharmacological manipulations of mTOR complex 1 (mTORC1) activity in hypothalamic neurons alter food intake and body weight. Our previous study identified Rheb1 (Ras homolog enriched in brain 1) as an essential activator of mTORC1 activity in the brain. Here we examine whether central Rheb1 regulates food intake and peripheral metabolism through mTORC1 signaling. We find that genetic deletion of Rheb1 in the brain causes a reduction in mTORC1 activity and impairs normal food intake. As a result, Rheb1 knockout mice exhibit hypoglycemia and increased lipid mobilization in adipose tissue and ketogenesis in the liver. Our work highlights the importance of central Rheb1 signaling in euglycemia and energy homeostasis in animals. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Temperature-Responsive Poly(ε-caprolactone) Cell Culture Platform with Dynamically Tunable Nano-Roughness and Elasticity for Control of Myoblast Morphology
Int. J. Mol. Sci. 2014, 15(1), 1511-1524; doi:10.3390/ijms15011511
Received: 6 December 2013 / Revised: 15 January 2014 / Accepted: 16 January 2014 / Published: 21 January 2014
Cited by 13 | PDF Full-text (1154 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
We developed a dynamic cell culture platform with dynamically tunable nano-roughness and elasticity. Temperature-responsive poly(ε-caprolactone) (PCL) films were successfully prepared by crosslinking linear and tetra-branched PCL macromonomers. By optimizing the mixing ratios, the crystal-amorphous transition temperature (Tm) of the [...] Read more.
We developed a dynamic cell culture platform with dynamically tunable nano-roughness and elasticity. Temperature-responsive poly(ε-caprolactone) (PCL) films were successfully prepared by crosslinking linear and tetra-branched PCL macromonomers. By optimizing the mixing ratios, the crystal-amorphous transition temperature (Tm) of the crosslinked film was adjusted to the biological relevant temperature (~33 °C). While the crosslinked films are relatively stiff (50 MPa) below the Tm, they suddenly become soft (1 MPa) above the Tm. Correspondingly, roughness of the surface was decreased from 63.4–12.4 nm. It is noted that the surface wettability was independent of temperature. To investigate the role of dynamic surface roughness and elasticity on cell adhesion, cells were seeded on PCL films at 32 °C. Interestingly, spread myoblasts on the film became rounded when temperature was suddenly increased to 37 °C, while significant changes in cell morphology were not observed for fibroblasts. These results indicate that cells can sense dynamic changes in the surrounding environment but the sensitivity depends on cell types. Full article
(This article belongs to the Special Issue Interaction between Nano-Structure Materials and Cells)
Open AccessArticle Role of Insulin-Transferrin-Selenium in Auricular Chondrocyte Proliferation and Engineered Cartilage Formation in Vitro
Int. J. Mol. Sci. 2014, 15(1), 1525-1537; doi:10.3390/ijms15011525
Received: 26 November 2013 / Revised: 7 January 2014 / Accepted: 8 January 2014 / Published: 21 January 2014
Cited by 2 | PDF Full-text (639 KB) | HTML Full-text | XML Full-text
Abstract
The goal of this study is to determine the effects of Insulin-Transferrin-Selenium (ITS) on proliferation of auricular chondrocytes and formation of engineered cartilage in vitro. Pig auricular monolayer chondrocytes and chondrocyte pellets were cultured in media containing 1% ITS at different [...] Read more.
The goal of this study is to determine the effects of Insulin-Transferrin-Selenium (ITS) on proliferation of auricular chondrocytes and formation of engineered cartilage in vitro. Pig auricular monolayer chondrocytes and chondrocyte pellets were cultured in media containing 1% ITS at different concentrations of fetal bovine serum (FBS, 10%, 6%, 2%, 0%), or 10% FBS alone as a control for four weeks. Parameters including cell proliferation in monolayer, wet weight, collagen type I/II/X (Col I, II, X) and glycosaminoglycan (GAG) expression, GAG content of pellets and gene expression associated with cartilage formation/dedifferentiation (lost cartilage phenotype)/hypertrophy within the chondrocyte pellets were assessed. The results showed that chondrocytes proliferation rates increased when FBS concentrations increased (2%, 6%, 10% FBS) in ITS supplemented groups. In addition, 1% ITS plus 10% FBS significantly promoted cell proliferation than 10% FBS alone. No chondrocytes grew in ITS alone medium. 1% ITS plus 10% FBS enhanced cartilage formation in terms of size, wet weight, cartilage specific matrices, and homogeneity, compared to 10% FBS alone group. Furthermore, ITS prevented engineered cartilage from dedifferentiation (i.e., higher index of Col II/Col I mRNA expression and expression of aggrecan) and hypertrophy (i.e., lower mRNA expression of Col X and MMP13). In conclusion, our results indicated that ITS efficiently enhanced auricular chondrocytes proliferation, retained chondrogenic phenotypes, and promoted engineered cartilage formation when combined with FBS, which is potentially used as key supplementation in auricular chondrocytes and engineered cartilage culture. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Egr-1 Upregulates Siva-1 Expression and Induces Cardiac Fibroblast Apoptosis
Int. J. Mol. Sci. 2014, 15(1), 1538-1553; doi:10.3390/ijms15011538
Received: 9 December 2013 / Revised: 21 December 2013 / Accepted: 13 January 2014 / Published: 21 January 2014
Cited by 3 | PDF Full-text (1380 KB) | HTML Full-text | XML Full-text
Abstract
The early growth response transcription factor Egr-1 controls cell specific responses to proliferation, differentiation and apoptosis. Expression of Egr-1 and downstream transcription is closely controlled and cell specific upregulation induced by processes such as hypoxia and ischemia has been previously linked to [...] Read more.
The early growth response transcription factor Egr-1 controls cell specific responses to proliferation, differentiation and apoptosis. Expression of Egr-1 and downstream transcription is closely controlled and cell specific upregulation induced by processes such as hypoxia and ischemia has been previously linked to multiple aspects of cardiovascular injury. In this study, we showed constitutive expression of Egr-1 in cultured human ventricular cardiac fibroblasts, used adenoviral mediated gene transfer to study the effects of continuous Egr-1 overexpression and studied downstream transcription by Western blotting, immunohistochemistry and siRNA transfection. Apoptosis was assessed by fluorescence microscopy and flow cytometry in the presence of caspase inhibitors. Overexpression of Egr-1 directly induced apoptosis associated with caspase activation in human cardiac fibroblast cultures in vitro assessed by fluorescence microscopy and flow cytometry. Apoptotic induction was associated with a caspase activation associated loss of mitochondrial membrane potential and transient downstream transcriptional up-regulation of the pro-apoptotic gene product Siva-1. Suppression of Siva-1 induction by siRNA partially reversed Egr-1 mediated loss of cell viability. These findings suggest a previously unknown role for Egr-1 and transcriptional regulation of Siva-1 in the control of cardiac accessory cell death. Full article
(This article belongs to the collection Programmed Cell Death and Apoptosis)
Open AccessArticle Phosphorylation of Histone H2AX in the Mouse Brain from Development to Senescence
Int. J. Mol. Sci. 2014, 15(1), 1554-1573; doi:10.3390/ijms15011554
Received: 12 November 2013 / Revised: 30 December 2013 / Accepted: 10 January 2014 / Published: 21 January 2014
Cited by 4 | PDF Full-text (2771 KB) | HTML Full-text | XML Full-text
Abstract
Phosphorylation of the histone H2AX (γH2AX form) is an early response to DNA damage and a marker of aging and disease in several cells and tissues outside the nervous system. Little is known about in vivo phosphorylation of H2AX in neurons, although [...] Read more.
Phosphorylation of the histone H2AX (γH2AX form) is an early response to DNA damage and a marker of aging and disease in several cells and tissues outside the nervous system. Little is known about in vivo phosphorylation of H2AX in neurons, although it was suggested that γH2AX is an early marker of neuronal endangerment thus opening the possibility to target it as a neuroprotective strategy. After experimental labeling of DNA-synthesizing cells with 5-bromo-2-deoxyuridine (BrdU), we studied the brain occurrence of γH2AX in developing, postnatal, adult and senescent (2 years) mice by light and electron microscopic immunocytochemistry and Western blotting. Focal and/or diffuse γH2AX immunostaining appears in interkinetic nuclei, mitotic chromosomes, and apoptotic nuclei. Immunoreactivity is mainly associated with neurogenetic areas, i.e., the subventricular zone (SVZ) of telencephalon, the cerebellar cortex, and, albeit to a much lesser extent, the subgranular zone of the hippocampal dentate gyrus. In addition, γH2AX is highly expressed in the adult and senescent cerebral cortex, particularly the piriform cortex. Double labeling experiments demonstrate that γH2AX in neurogenetic brain areas is temporally and functionally related to proliferation and apoptosis of neuronal precursors, i.e., the type C transit amplifying cells (SVZ) and the granule cell precursors (cerebellum). Conversely, γH2AX-immunoreactive cortical neurons incorporating the S phase-label BrdU do not express the proliferation marker phosphorylated histone H3, indicating that these postmitotic cells undergo a significant DNA damage response. Our study paves the way for a better comprehension of the role of H2AX phosphorylation in the normal brain, and offers additional data to design novel strategies for the protection of neuronal precursors and mature neurons in central nervous system (CNS) degenerative diseases. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2014)
Open AccessArticle Genetic Variants of GPER/GPR30, a Novel Estrogen-Related G Protein Receptor, Are Associated with Human Seminoma
Int. J. Mol. Sci. 2014, 15(1), 1574-1589; doi:10.3390/ijms15011574
Received: 25 November 2013 / Revised: 16 December 2013 / Accepted: 3 January 2014 / Published: 21 January 2014
Cited by 8 | PDF Full-text (685 KB) | HTML Full-text | XML Full-text
Abstract
Testicular germ cell tumors (TGCTs) are the most common solid cancers in young men, with an increasing incidence over several years. However, their pathogenesis remains a matter of debate. Some epidemiological data suggest the involvement of both environmental and genetic factors. We [...] Read more.
Testicular germ cell tumors (TGCTs) are the most common solid cancers in young men, with an increasing incidence over several years. However, their pathogenesis remains a matter of debate. Some epidemiological data suggest the involvement of both environmental and genetic factors. We reported two distinct effects of estrogens and/or xeno-estrogens on in vitro human seminoma-derived cells proliferation: (1) an antiproliferative effect via a classical estrogen receptor beta-dependent pathway, and (2) a promotive effect via a non-classical membrane G-protein-coupled receptor, GPR30/GPER, which is only overexpressed in seminomas, the most common TGCT. In order to explain this overexpression, we investigated the possible association of polymorphisms in the GPER gene by using allele-specific tetra-primer polymerase chain reaction performed on tissue samples from 150 paraffin-embedded TGCT specimens (131 seminomas, 19 non seminomas). Compared to control population, loss of homozygous ancestral genotype GG in two polymorphisms located in the promoter region of GPER (rs3808350 and rs3808351) was more frequent in seminomas but not in non-seminomas (respectively, OR = 1.960 (1.172–3.277) and 7.000 (2.747–17.840); p < 0.01). These polymorphisms may explain GPER overexpression and represent a genetic factor of susceptibility supporting the contribution of environmental GPER ligands in testicular carcinogenesis. Full article
(This article belongs to the collection G Protein-Coupled Receptor Signaling and Regulation)
Figures

Open AccessArticle Magnetic Nanoparticles as Intraocular Drug Delivery System to Target Retinal Pigmented Epithelium (RPE)
Int. J. Mol. Sci. 2014, 15(1), 1590-1605; doi:10.3390/ijms15011590
Received: 9 December 2013 / Revised: 3 January 2014 / Accepted: 6 January 2014 / Published: 22 January 2014
Cited by 4 | PDF Full-text (1066 KB) | HTML Full-text | XML Full-text
Abstract
One of the most challenging efforts in drug delivery is the targeting of the eye. The eye structure and barriers render this organ poorly permeable to drugs. Quite recently the entrance of nanoscience in ocular drug delivery has improved the penetration and [...] Read more.
One of the most challenging efforts in drug delivery is the targeting of the eye. The eye structure and barriers render this organ poorly permeable to drugs. Quite recently the entrance of nanoscience in ocular drug delivery has improved the penetration and half-life of drugs, especially in the anterior eye chamber, while targeting the posterior chamber is still an open issue. The retina and the retinal pigment epithelium/choroid tissues, located in the posterior eye chamber, are responsible for the majority of blindness both in childhood and adulthood. In the present study, we used magnetic nanoparticles (MNPs) as a nanotool for ocular drug delivery that is capable of specific localization in the retinal pigmented epithelium (RPE) layer. We demonstrate that, following intraocular injection in Xenopus embryos, MNPs localize specifically in RPE where they are retained for several days. The specificity of the localization did not depend on particle size and surface properties of the MNPs used in this work. Moreover, through similar experiments in zebrafish, we demonstrated that the targeting of RPE by the nanoparticles is not specific for the Xenopus species. Full article
(This article belongs to the Special Issue Interaction between Nano-Structure Materials and Cells)
Figures

Open AccessArticle Intravitreal Injection of Ranibizumab and CTGF shRNA Improves Retinal Gene Expression and Microvessel Ultrastructure in a Rodent Model of Diabetes
Int. J. Mol. Sci. 2014, 15(1), 1606-1624; doi:10.3390/ijms15011606
Received: 1 November 2013 / Revised: 10 January 2014 / Accepted: 13 January 2014 / Published: 22 January 2014
Cited by 13 | PDF Full-text (4268 KB) | HTML Full-text | XML Full-text
Abstract
Therapeutic modalities targeting vascular endothelial growth factor (VEGF) have been used to treat neovascularization and macular edema. However, anti-VEGF treatment alone may cause up-regulation of connective tissue growth factor (CTGF) in the retina, increasing the risk of fibrosis and tractional retinal detachment. [...] Read more.
Therapeutic modalities targeting vascular endothelial growth factor (VEGF) have been used to treat neovascularization and macular edema. However, anti-VEGF treatment alone may cause up-regulation of connective tissue growth factor (CTGF) in the retina, increasing the risk of fibrosis and tractional retinal detachment. Therefore, in this study, we employ a novel dual-target intervention that involves intravitreal injection of the VEGF inhibitor ranibizumab and a transfection reagent-treated non-viral vector carrying anti-CTGF short hairpin RNA (shRNA) driven by human RNA polymerase III promoter U6. The effects of the dual-target intervention on the expression of VEGF and CTGF and on microvessel ultrastructure were examined in retina of streptozocin-induced diabetic rats. CTGF was significantly up-regulated at week 8 after diabetic induction, whereas VEGF was not up-regulated until week 10. The high expression of both genes was maintained at week 12. Transmission electron microscopy also revealed progressive exacerbation of microvessel ultrastructure during the same period. In addition, ranibizumab significantly lowered VEGF but elevated CTGF mRNA, whereas CTGF shRNA significantly reduced the mRNA levels of both CTGF and VEGF in diabetic retinas. Importantly, dual-target intervention normalized the transcript levels of both target genes and ameliorated retinal microvessel ultrastructural damage better than either single-target intervention. These results suggest the advantages of dual-target over single-target interventions in diabetic retina and reveal a novel therapeutic modality for diabetic retinopathy. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Figures

Open AccessArticle Resveratrol Partially Prevents Rotenone-Induced Neurotoxicity in Dopaminergic SH-SY5Y Cells through Induction of Heme Oxygenase-1 Dependent Autophagy
Int. J. Mol. Sci. 2014, 15(1), 1625-1646; doi:10.3390/ijms15011625
Received: 11 November 2013 / Revised: 8 January 2014 / Accepted: 14 January 2014 / Published: 22 January 2014
Cited by 31 | PDF Full-text (1283 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Parkinson disease (PD) is a complex neurodegenerative disorder characterized by a progressive loss of dopaminergic neurons. Mitochondrial dysfunction, oxidative stress or protein misfolding and aggregation may underlie this process. Autophagy is an intracellular catabolic mechanism responsible for protein degradation and recycling of [...] Read more.
Parkinson disease (PD) is a complex neurodegenerative disorder characterized by a progressive loss of dopaminergic neurons. Mitochondrial dysfunction, oxidative stress or protein misfolding and aggregation may underlie this process. Autophagy is an intracellular catabolic mechanism responsible for protein degradation and recycling of damaged proteins and cytoplasmic organelles. Autophagic dysfunction may hasten the progression of neuronal degeneration. In this study, resveratrol promoted autophagic flux and protected dopaminergic neurons against rotenone-induced apoptosis. In an in vivo PD model, rotenone induced loss of dopaminergic neurons, increased oxidation of mitochondrial proteins and promoted autophagic vesicle development in brain tissue. The natural phytoalexin resveratrol prevented rotenone-induced neuronal apoptosis in vitro, and this pro-survival effect was abolished by an autophagic inhibitor. Although both rotenone and resveratrol promoted LC3-II accumulation, autophagic flux was inhibited by rotenone and augmented by resveratrol. Further, rotenone reduced heme oxygenase-1 (HO-1) expression, whereas resveratrol increased HO-1 expression. Pharmacological inhibition of HO-1 abolished resveratrol-mediated autophagy and neuroprotection. Notably, the effects of a pharmacological inducer of HO-1 were similar to those of resveratrol, and protected against rotenone-induced cell death in an autophagy-dependent manner, validating the hypothesis of HO-1 dependent autophagy in preventing neuronal death in the in vitro PD model. Collectively, our findings suggest that resveratrol induces HO-1 expression and prevents dopaminergic cell death by regulating autophagic flux; thus protecting against rotenone-induced neuronal apoptosis. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2014)
Open AccessArticle The hOGG1 Ser326Cys Gene Polymorphism and the Risk of Coronary Ectasia in the Chinese Population
Int. J. Mol. Sci. 2014, 15(1), 1671-1682; doi:10.3390/ijms15011671
Received: 14 November 2013 / Revised: 6 January 2014 / Accepted: 20 January 2014 / Published: 22 January 2014
Cited by 3 | PDF Full-text (314 KB) | HTML Full-text | XML Full-text
Abstract
Oxidative stress (OS) is related to vascular inflammation possibly, contributing to the development of coronary ectasia (CE). Base excision repair (BER) and nucleotide excision repair are the main DNA repair pathways that can help to remove 8-hydroxydeoxyguanine (8-OHdG), a marker of OS. [...] Read more.
Oxidative stress (OS) is related to vascular inflammation possibly, contributing to the development of coronary ectasia (CE). Base excision repair (BER) and nucleotide excision repair are the main DNA repair pathways that can help to remove 8-hydroxydeoxyguanine (8-OHdG), a marker of OS. Human 8-oxoguanine DNA glycosylase 1 (hOGG1) is a key enzyme of the BER pathway and catalyzes the removal of 8-OHdG. The aim of our study was to investigate the association between hOGG1 Ser326Cys gene polymorphism and CE in a Chinese population. Five-hundred forty-seven patients who underwent diagnostic coronary angiography in a tertiary medical center were recruited. The angiographic definition of CE is the diameter of the ectatic segment being more than 1.5 times larger compared with an adjacent healthy reference segment. The gene polymorphisms were analyzed by polymerase chain reaction. The urine 8OHdG concentration was measured using a commercial ELISA kit. The distribution of hOGG1 Ser326Cys genotypes was significantly different between CE and non-CE groups (p = 0.033). The odds ratio of CE development for the Ser to the Cys variant was 1.55 (95% confidence interval (CI), 1.04–2.31, p = 0.033). Both univariate and logistic regression analysis showed a significant association of hOGG1 Ser326Cys polymorphism in the dominant model with CE development (p = 0.009 and 0.011, respectively). Urine 8-OHdG levels were significantly higher in subjects carrying the hOGG1 Ser variant than in those with the Cys/Cys genotype (p < 0.03). In conclusion, our study suggests that the hOGG1 Ser326Cys gene variant might play a role in susceptibility to the development of CE. Full article
(This article belongs to the collection Human Single Nucleotide Polymorphisms and Disease Diagnostics)

Review

Jump to: Editorial, Research, Other

Open AccessReview Chloride Channelopathies of ClC-2
Int. J. Mol. Sci. 2014, 15(1), 218-249; doi:10.3390/ijms15010218
Received: 26 September 2013 / Revised: 14 November 2013 / Accepted: 16 December 2013 / Published: 27 December 2013
PDF Full-text (632 KB) | HTML Full-text | XML Full-text
Abstract
Chloride channels (ClCs) have gained worldwide interest because of their molecular diversity, widespread distribution in mammalian tissues and organs, and their link to various human diseases. Nine different ClCs have been molecularly identified and functionally characterized in mammals. ClC-2 is one of [...] Read more.
Chloride channels (ClCs) have gained worldwide interest because of their molecular diversity, widespread distribution in mammalian tissues and organs, and their link to various human diseases. Nine different ClCs have been molecularly identified and functionally characterized in mammals. ClC-2 is one of nine mammalian members of the ClC family. It possesses unique biophysical characteristics, pharmacological properties, and molecular features that distinguish it from other ClC family members. ClC-2 has wide organ/tissue distribution and is ubiquitously expressed. Published studies consistently point to a high degree of conservation of ClC-2 function and regulation across various species from nematodes to humans over vast evolutionary time spans. ClC-2 has been intensively and extensively studied over the past two decades, leading to the accumulation of a plethora of information to advance our understanding of its pathophysiological functions; however, many controversies still exist. It is necessary to analyze the research findings, and integrate different views to have a better understanding of ClC-2. This review focuses on ClC-2 only, providing an analytical overview of the available literature. Nearly every aspect of ClC-2 is discussed in the review: molecular features, biophysical characteristics, pharmacological properties, cellular function, regulation of expression and function, and channelopathies. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessReview Traumatic Brain Injury Pathophysiology and Treatments: Early, Intermediate, and Late Phases Post-Injury
Int. J. Mol. Sci. 2014, 15(1), 309-341; doi:10.3390/ijms15010309
Received: 10 November 2013 / Revised: 2 December 2013 / Accepted: 20 December 2013 / Published: 30 December 2013
Cited by 41 | PDF Full-text (375 KB) | HTML Full-text | XML Full-text
Abstract
Traumatic Brain Injury (TBI) affects a large proportion and extensive array of individuals in the population. While precise pathological mechanisms are lacking, the growing base of knowledge concerning TBI has put increased emphasis on its understanding and treatment. Most treatments of TBI [...] Read more.
Traumatic Brain Injury (TBI) affects a large proportion and extensive array of individuals in the population. While precise pathological mechanisms are lacking, the growing base of knowledge concerning TBI has put increased emphasis on its understanding and treatment. Most treatments of TBI are aimed at ameliorating secondary insults arising from the injury; these insults can be characterized with respect to time post-injury, including early, intermediate, and late pathological changes. Early pathological responses are due to energy depletion and cell death secondary to excitotoxicity, the intermediate phase is characterized by neuroinflammation and the late stage by increased susceptibility to seizures and epilepsy. Current treatments of TBI have been tailored to these distinct pathological stages with some overlap. Many prophylactic, pharmacologic, and surgical treatments are used post-TBI to halt the progression of these pathologic reactions. In the present review, we discuss the mechanisms of the pathological hallmarks of TBI and both current and novel treatments which target the respective pathways. Full article
(This article belongs to the Special Issue Pathology and Treatment of Central Nervous System Diseases)
Open AccessReview Chemokine Receptors in Epithelial Ovarian Cancer
Int. J. Mol. Sci. 2014, 15(1), 361-376; doi:10.3390/ijms15010361
Received: 2 December 2013 / Revised: 17 December 2013 / Accepted: 19 December 2013 / Published: 31 December 2013
Cited by 5 | PDF Full-text (376 KB) | HTML Full-text | XML Full-text
Abstract
Ovarian carcinoma is the deadliest gynecologic malignancy with very poor rate of survival, and it is characterized by the presence of vast incurable peritoneal metastasis. Studies of the role of chemokine receptors, a family of proteins belonging to the group of G [...] Read more.
Ovarian carcinoma is the deadliest gynecologic malignancy with very poor rate of survival, and it is characterized by the presence of vast incurable peritoneal metastasis. Studies of the role of chemokine receptors, a family of proteins belonging to the group of G protein-coupled receptors, in ovarian carcinoma strongly placed this family of membrane receptors as major regulators of progression of this malignancy. In this review, we will discuss the roles that chemokine-receptor interactions play to support angiogenesis, cell proliferation, migration, adhesion, invasion, metastasis, and immune evasion in progression of ovarian carcinoma. Data regarding the role that the chemokine receptors play in the disease progression accumulated insofar strongly suggest that this family of proteins could be good therapeutic targets against ovarian carcinoma. Full article
(This article belongs to the collection G Protein-Coupled Receptor Signaling and Regulation)
Open AccessReview Multi-Scale Computational Enzymology: Enhancing Our Understanding of Enzymatic Catalysis
Int. J. Mol. Sci. 2014, 15(1), 401-422; doi:10.3390/ijms15010401
Received: 11 November 2013 / Revised: 5 December 2013 / Accepted: 24 December 2013 / Published: 31 December 2013
Cited by 1 | PDF Full-text (858 KB) | HTML Full-text | XML Full-text
Abstract
Elucidating the origin of enzymatic catalysis stands as one the great challenges of contemporary biochemistry and biophysics. The recent emergence of computational enzymology has enhanced our atomistic-level description of biocatalysis as well the kinetic and thermodynamic properties of their mechanisms. There exists [...] Read more.
Elucidating the origin of enzymatic catalysis stands as one the great challenges of contemporary biochemistry and biophysics. The recent emergence of computational enzymology has enhanced our atomistic-level description of biocatalysis as well the kinetic and thermodynamic properties of their mechanisms. There exists a diversity of computational methods allowing the investigation of specific enzymatic properties. Small or large density functional theory models allow the comparison of a plethora of mechanistic reactive species and divergent catalytic pathways. Molecular docking can model different substrate conformations embedded within enzyme active sites and determine those with optimal binding affinities. Molecular dynamics simulations provide insights into the dynamics and roles of active site components as well as the interactions between substrate and enzymes. Hybrid quantum mechanical/molecular mechanical (QM/MM) can model reactions in active sites while considering steric and electrostatic contributions provided by the surrounding environment. Using previous studies done within our group, on OvoA, EgtB, ThrRS, LuxS and MsrA enzymatic systems, we will review how these methods can be used either independently or cooperatively to get insights into enzymatic catalysis. Full article
Open AccessReview Acyl-Homoserine Lactone Quorum Sensing in the Roseobacter Clade
Int. J. Mol. Sci. 2014, 15(1), 654-669; doi:10.3390/ijms15010654
Received: 28 October 2013 / Revised: 15 December 2013 / Accepted: 18 December 2013 / Published: 7 January 2014
Cited by 14 | PDF Full-text (429 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Members of the Roseobacter clade are ecologically important and numerically abundant in coastal environments and can associate with marine invertebrates and nutrient-rich marine snow or organic particles, on which quorum sensing (QS) may play an important role. In this review, we summarize [...] Read more.
Members of the Roseobacter clade are ecologically important and numerically abundant in coastal environments and can associate with marine invertebrates and nutrient-rich marine snow or organic particles, on which quorum sensing (QS) may play an important role. In this review, we summarize current research progress on roseobacterial acyl-homoserine lactone-based QS, particularly focusing on three relatively well-studied representatives, Phaeobacter inhibens DSM17395, the marine sponge symbiont Ruegeria sp. KLH11 and the dinoflagellate symbiont Dinoroseobacter shibae. Bioinformatic survey of luxI homologues revealed that over 80% of available roseobacterial genomes encode at least one luxI homologue, reflecting the significance of QS controlled regulatory pathways in adapting to the relevant marine environments. We also discuss several areas that warrant further investigation, including studies on the ecological role of these diverse QS pathways in natural environments. Full article
(This article belongs to the Special Issue Quorum Sensing Research in Microbial Systems)
Open AccessReview Meta-Omic Platforms to Assist in the Understanding of NAFLD Gut Microbiota Alterations: Tools and Applications
Int. J. Mol. Sci. 2014, 15(1), 684-711; doi:10.3390/ijms15010684
Received: 10 November 2013 / Revised: 29 December 2013 / Accepted: 2 January 2014 / Published: 7 January 2014
Cited by 5 | PDF Full-text (1250 KB) | HTML Full-text | XML Full-text
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease worldwide as a result of the increasing prevalence of obesity, starting from early life stages. It is characterized by a spectrum of liver diseases ranging from simple fatty [...] Read more.
Non-alcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease worldwide as a result of the increasing prevalence of obesity, starting from early life stages. It is characterized by a spectrum of liver diseases ranging from simple fatty liver (NAFL) to steatohepatitis (NASH), with a possible progression to fibrosis, thus increasing liver-related morbidity and mortality. NAFLD development is driven by the co-action of several risk factors, including obesity and metabolic syndrome, which may be both genetically induced and diet-related. Recently, particular attention has been paid to the gut-liver axis, which may play a physio-pathological role in the onset and progression of the disease. The gut microbiota is intended to act as a bioreactor that can guarantee autonomous metabolic and immunological functions and that can drive functional strategies within the environment of the body in response to external stimuli. The complexity of the gut microbiota suggests that it behaves as an organ. Therefore, the concept of the gut-liver axis must be complemented with the gut-microbiota-liver network due to the high intricacy of the microbiota components and metabolic activities; these activities form the active diet-driven power plant of the host. Such complexity can only be revealed using systems biology, which can integrate clinical phenomics and gut microbiota data. Full article
(This article belongs to the Special Issue Non-Alcoholic Fatty Liver Disease Research)
Open AccessReview The Effect of Radiation on the Immune Response to Cancers
Int. J. Mol. Sci. 2014, 15(1), 927-943; doi:10.3390/ijms15010927
Received: 21 October 2013 / Revised: 26 December 2013 / Accepted: 31 December 2013 / Published: 10 January 2014
Cited by 21 | PDF Full-text (465 KB) | HTML Full-text | XML Full-text
Abstract
In cancer patients undergoing radiation therapy, the beneficial effects of radiation can extend beyond direct cytotoxicity to tumor cells. Delivery of localized radiation to tumors often leads to systemic responses at distant sites, a phenomenon known as the abscopal effect which has [...] Read more.
In cancer patients undergoing radiation therapy, the beneficial effects of radiation can extend beyond direct cytotoxicity to tumor cells. Delivery of localized radiation to tumors often leads to systemic responses at distant sites, a phenomenon known as the abscopal effect which has been attributed to the induction and enhancement of the endogenous anti-tumor innate and adaptive immune response. The mechanisms surrounding the abscopal effect are diverse and include trafficking of lymphocytes into the tumor microenvironment, enhanced tumor recognition and killing via up-regulation of tumor antigens and antigen presenting machinery and, induction of positive immunomodulatory pathways. Here, we discuss potential mechanisms of radiation-induced enhancement of the anti-tumor response through its effect on the host immune system and explore potential combinational immune-based strategies such as adoptive cellular therapy using ex vivo expanded NK and T cells as a means of delivering a potent effector population in the context of radiation-enhanced anti-tumor immune environment. Full article
(This article belongs to the collection Radiation Toxicity in Cells)
Open AccessReview The Function and Catalysis of 2-Oxoglutarate-Dependent Oxygenases Involved in Plant Flavonoid Biosynthesis
Int. J. Mol. Sci. 2014, 15(1), 1080-1095; doi:10.3390/ijms15011080
Received: 14 November 2013 / Revised: 26 December 2013 / Accepted: 29 December 2013 / Published: 15 January 2014
Cited by 9 | PDF Full-text (404 KB) | HTML Full-text | XML Full-text
Abstract
Flavonoids are secondary metabolites derived from phenylalanine and acetate metabolism. They fulfil a variety of functions in plants and have health benefits for humans. During the synthesis of the tricyclic flavonoid natural products in plants, oxidative modifications to the central C ring [...] Read more.
Flavonoids are secondary metabolites derived from phenylalanine and acetate metabolism. They fulfil a variety of functions in plants and have health benefits for humans. During the synthesis of the tricyclic flavonoid natural products in plants, oxidative modifications to the central C ring are catalyzed by four of FeII and 2-oxoglutarate dependent (2-ODD) oxygenases, namely flavone synthase I (FNS I), flavonol synthase (FLS), anthocyanidin synthase (ANS) and flavanone 3β-hydroxylase (FHT). FNS I, FLS and ANS are involved in desaturation of C2–C3 of flavonoids and FHT in hydroxylation of C3. FNS I, which is restricted to the Apiaceae species and in rice, is predicted to have evolved from FHT by duplication. Due to their sequence similarity and substrate specificity, FLS and ANS, which interact with the α surface of the substrate, belong to a group of dioxygenases having a broad substrate specificity, while FNS I and FHT are more selective, and interact with the naringenin β surface. Here, we summarize recent findings regarding the function of the four 2-ODD oxygenases and the relationship between their catalytic activity, their polypeptide sequence and their tertiary structure. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessReview G Protein-Coupled Receptors: What a Difference a ‘Partner’ Makes
Int. J. Mol. Sci. 2014, 15(1), 1112-1142; doi:10.3390/ijms15011112
Received: 4 December 2013 / Revised: 20 December 2013 / Accepted: 8 January 2014 / Published: 16 January 2014
Cited by 7 | PDF Full-text (1172 KB) | HTML Full-text | XML Full-text
Abstract
G protein-coupled receptors (GPCRs) are important cell signaling mediators, involved in essential physiological processes. GPCRs respond to a wide variety of ligands from light to large macromolecules, including hormones and small peptides. Unfortunately, mutations and dysregulation of GPCRs that induce a loss [...] Read more.
G protein-coupled receptors (GPCRs) are important cell signaling mediators, involved in essential physiological processes. GPCRs respond to a wide variety of ligands from light to large macromolecules, including hormones and small peptides. Unfortunately, mutations and dysregulation of GPCRs that induce a loss of function or alter expression can lead to disorders that are sometimes lethal. Therefore, the expression, trafficking, signaling and desensitization of GPCRs must be tightly regulated by different cellular systems to prevent disease. Although there is substantial knowledge regarding the mechanisms that regulate the desensitization and down-regulation of GPCRs, less is known about the mechanisms that regulate the trafficking and cell-surface expression of newly synthesized GPCRs. More recently, there is accumulating evidence that suggests certain GPCRs are able to interact with specific proteins that can completely change their fate and function. These interactions add on another level of regulation and flexibility between different tissue/cell-types. Here, we review some of the main interacting proteins of GPCRs. A greater understanding of the mechanisms regulating their interactions may lead to the discovery of new drug targets for therapy. Full article
(This article belongs to the collection G Protein-Coupled Receptor Signaling and Regulation)
Open AccessReview Neuroprotective Strategies for Traumatic Brain Injury: Improving Clinical Translation
Int. J. Mol. Sci. 2014, 15(1), 1216-1236; doi:10.3390/ijms15011216
Received: 11 December 2013 / Revised: 7 January 2014 / Accepted: 13 January 2014 / Published: 17 January 2014
Cited by 34 | PDF Full-text (234 KB) | HTML Full-text | XML Full-text
Abstract
Traumatic brain injury (TBI) induces secondary biochemical changes that contribute to delayed neuroinflammation, neuronal cell death, and neurological dysfunction. Attenuating such secondary injury has provided the conceptual basis for neuroprotective treatments. Despite strong experimental data, more than 30 clinical trials of neuroprotection [...] Read more.
Traumatic brain injury (TBI) induces secondary biochemical changes that contribute to delayed neuroinflammation, neuronal cell death, and neurological dysfunction. Attenuating such secondary injury has provided the conceptual basis for neuroprotective treatments. Despite strong experimental data, more than 30 clinical trials of neuroprotection in TBI patients have failed. In part, these failures likely reflect methodological differences between the clinical and animal studies, as well as inadequate pre-clinical evaluation and/or trial design problems. However, recent changes in experimental approach and advances in clinical trial methodology have raised the potential for successful clinical translation. Here we critically analyze the current limitations and translational opportunities for developing successful neuroprotective therapies for TBI. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2014)
Open AccessReview Molecular Basis of Cardiac Myxomas
Int. J. Mol. Sci. 2014, 15(1), 1315-1337; doi:10.3390/ijms15011315
Received: 12 December 2013 / Revised: 4 January 2014 / Accepted: 8 January 2014 / Published: 20 January 2014
Cited by 4 | PDF Full-text (4310 KB) | HTML Full-text | XML Full-text
Abstract
Cardiac tumors are rare, and of these, primary cardiac tumors are even rarer. Metastatic cardiac tumors are about 100 times more common than the primary tumors. About 90% of primary cardiac tumors are benign, and of these the most common are cardiac [...] Read more.
Cardiac tumors are rare, and of these, primary cardiac tumors are even rarer. Metastatic cardiac tumors are about 100 times more common than the primary tumors. About 90% of primary cardiac tumors are benign, and of these the most common are cardiac myxomas. Approximately 12% of primary cardiac tumors are completely asymptomatic while others present with one or more signs and symptoms of the classical triad of hemodynamic changes due to intracardiac obstruction, embolism and nonspecific constitutional symptoms. Echocardiography is highly sensitive and specific in detecting cardiac tumors. Other helpful investigations are chest X-rays, magnetic resonance imaging and computerized tomography scan. Surgical excision is the treatment of choice for primary cardiac tumors and is usually associated with a good prognosis. This review article will focus on the general features of benign cardiac tumors with an emphasis on cardiac myxomas and their molecular basis. Full article
(This article belongs to the Special Issue Molecular Bases of Cancer Research)
Figures

Open AccessReview In Silico Discovery of Aminoacyl-tRNA Synthetase Inhibitors
Int. J. Mol. Sci. 2014, 15(1), 1358-1373; doi:10.3390/ijms15011358
Received: 10 December 2013 / Revised: 2 January 2014 / Accepted: 7 January 2014 / Published: 20 January 2014
Cited by 5 | PDF Full-text (520 KB) | HTML Full-text | XML Full-text
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyze the transfer of amino acids to their cognate tRNA. They play a pivotal role in protein synthesis and are essential for cell growth and survival. The aaRSs are one of the leading targets for development [...] Read more.
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyze the transfer of amino acids to their cognate tRNA. They play a pivotal role in protein synthesis and are essential for cell growth and survival. The aaRSs are one of the leading targets for development of antibiotic agents. In this review, we mainly focused on aaRS inhibitor discovery and development using in silico methods including virtual screening and structure-based drug design. These computational methods are relatively fast and cheap, and are proving to be of great benefit for the rational development of more potent aaRS inhibitors and other pharmaceutical agents that may usher in a much needed generation of new antibiotics. Full article
Open AccessReview Beyond the Role of Dietary Protein and Amino Acids in the Prevention of Diet-Induced Obesity
Int. J. Mol. Sci. 2014, 15(1), 1374-1391; doi:10.3390/ijms15011374
Received: 11 November 2013 / Revised: 9 January 2014 / Accepted: 9 January 2014 / Published: 20 January 2014
Cited by 6 | PDF Full-text (2087 KB) | HTML Full-text | XML Full-text
Abstract
High-protein diets have been shown to prevent the development of diet-induced obesity and can improve associated metabolic disorders in mice. Dietary leucine supplementation can partially mimic this effect. However, the molecular mechanisms triggering these preventive effects remain to be satisfactorily explained. Here [...] Read more.
High-protein diets have been shown to prevent the development of diet-induced obesity and can improve associated metabolic disorders in mice. Dietary leucine supplementation can partially mimic this effect. However, the molecular mechanisms triggering these preventive effects remain to be satisfactorily explained. Here we review studies showing a connection between high protein or total amino nitrogen intake and obligatory water intake. High amino nitrogen intake may possibly lower lipid storage, and prevent insulin resistance. Suggestions are made for further systematical studies to explore the relationship between water consumption, satiety, and energy expenditure. Moreover, these examinations should better distinguish between leucine-specific and unspecific effects. Research in this field can provide important information to justify dietary recommendations and strategies in promoting long-term weight loss and may help to reduce health problems associated with the comorbidities of obesity. Full article
(This article belongs to the Special Issue Nutritional Control of Metabolism)
Open AccessReview Secondary Plant Products Causing Photosensitization in Grazing Herbivores: Their Structure, Activity and Regulation
Int. J. Mol. Sci. 2014, 15(1), 1441-1465; doi:10.3390/ijms15011441
Received: 15 December 2013 / Revised: 31 December 2013 / Accepted: 14 January 2014 / Published: 21 January 2014
Cited by 9 | PDF Full-text (537 KB) | HTML Full-text | XML Full-text
Abstract
Photosensitivity in animals is defined as a severe dermatitis that results from a heightened reactivity of skin cells and associated dermal tissues upon their exposure to sunlight, following ingestion or contact with UV reactive secondary plant products. Photosensitivity occurs in animal cells [...] Read more.
Photosensitivity in animals is defined as a severe dermatitis that results from a heightened reactivity of skin cells and associated dermal tissues upon their exposure to sunlight, following ingestion or contact with UV reactive secondary plant products. Photosensitivity occurs in animal cells as a reaction that is mediated by a light absorbing molecule, specifically in this case a plant-produced metabolite that is heterocyclic or polyphenolic. In sensitive animals, this reaction is most severe in non-pigmented skin which has the least protection from UV or visible light exposure. Photosensitization in a biological system such as the epidermis is an oxidative or other chemical change in a molecule in response to light-induced excitation of endogenous or exogenously-delivered molecules within the tissue. Photo-oxidation can also occur in the plant itself, resulting in the generation of reactive oxygen species, free radical damage and eventual DNA degradation. Similar cellular changes occur in affected herbivores and are associated with an accumulation of photodynamic molecules in the affected dermal tissues or circulatory system of the herbivore. Recent advances in our ability to identify and detect secondary products at trace levels in the plant and surrounding environment, or in organisms that ingest plants, have provided additional evidence for the role of secondary metabolites in photosensitization of grazing herbivores. This review outlines the role of unique secondary products produced by higher plants in the animal photosensitization process, describes their chemistry and localization in the plant as well as impacts of the environment upon their production, discusses their direct and indirect effects on associated animal systems and presents several examples of well-characterized plant photosensitization in animal systems. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessReview Signaling Involved in Hair Follicle Morphogenesis and Development
Int. J. Mol. Sci. 2014, 15(1), 1647-1670; doi:10.3390/ijms15011647
Received: 10 August 2013 / Revised: 21 October 2013 / Accepted: 22 October 2013 / Published: 22 January 2014
Cited by 18 | PDF Full-text (415 KB) | HTML Full-text | XML Full-text
Abstract
Hair follicle morphogenesis depends on Wnt, Shh, Notch, BMP and other signaling pathways interplay between epithelial and mesenchymal cells. The Wnt pathway plays an essential role during hair follicle induction, Shh is involved in morphogenesis and late stage differentiation, Notch signaling determines [...] Read more.
Hair follicle morphogenesis depends on Wnt, Shh, Notch, BMP and other signaling pathways interplay between epithelial and mesenchymal cells. The Wnt pathway plays an essential role during hair follicle induction, Shh is involved in morphogenesis and late stage differentiation, Notch signaling determines stem cell fate while BMP is involved in cellular differentiation. The Wnt pathway is considered to be the master regulator during hair follicle morphogenesis. Wnt signaling proceeds through EDA/EDAR/NF-κB signaling. NF-κB regulates the Wnt pathway and acts as a signal mediator by upregulating the expression of Shh ligand. Signal crosstalk between epithelial and mesenchymal cells takes place mainly through primary cilia. Primary cilia formation is initiated with epithelial laminin-511 interaction with dermal β-1 integrin, which also upregulates expression of downstream effectors of Shh pathway in dermal lineage. PDGF signal transduction essential for crosstalk is mediated through epithelial PDGF-A and PDGFRα expressed on the primary cilia. Dermal Shh and PDGF signaling up-regulates dermal noggin expression; noggin is a potent inhibitor of BMP signaling which helps in counteracting BMP mediated β-catenin inhibition. This interplay of signaling between the epithelial and dermal lineage helps in epithelial Shh signal amplification. The dermal Wnt pathway helps in upregulation of epithelial Notch expression. Dysregulation of these pathways leads to certain abnormalities and in some cases even tumor outgrowth. Full article
(This article belongs to the Special Issue Molecular Research of Epidermal Stem Cells)

Other

Jump to: Editorial, Research, Review

Open AccessTechnical Note Cellulase Activity Screening Using Pure Carboxymethylcellulose: Application to Soluble Cellulolytic Samples and to Plant Tissue Prints
Int. J. Mol. Sci. 2014, 15(1), 830-838; doi:10.3390/ijms15010830
Received: 9 December 2013 / Revised: 2 January 2014 / Accepted: 6 January 2014 / Published: 9 January 2014
Cited by 10 | PDF Full-text (996 KB) | HTML Full-text | XML Full-text
Abstract
Reliable, rapid and inexpensive detection of cellulolytic enzymes that can be used for a wide variety of biological and environmental samples are currently in high demand. Here, a new cellulase detection protocol is described that circumvents problems observed with popular agar-based methods [...] Read more.
Reliable, rapid and inexpensive detection of cellulolytic enzymes that can be used for a wide variety of biological and environmental samples are currently in high demand. Here, a new cellulase detection protocol is described that circumvents problems observed with popular agar-based methods by exploiting the ability of carboxymethylcellulose (CMC) to form gel-like surfaces on its own. These pure CMC-layers are sensitive to cellulolytic degradation and stainable by Gram’s iodine without showing unwelcome reactions with other enzymes. The staining intensity negatively correlates with the enzyme activity and can be used for quantification. Cellulase activities are not obstructed by high sugar contents (e.g., in plant material) which limit the applicability of other quantification methods, making our new method particularly attractive for screening of plant extracts. A useful variant of this new method is its applicability to plant tissue prints for spatial mapping of the cellulolytic activity in a zymogram-like fashion. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)

Journal Contact

MDPI AG
IJMS Editorial Office
St. Alban-Anlage 66, 4052 Basel, Switzerland
ijms@mdpi.com
Tel. +41 61 683 77 34
Fax: +41 61 302 89 18
Editorial Board
Contact Details Submit to IJMS
Back to Top